Recently an article on BreakPoint0, Bombing Mary, was published. I'm going to attempt to address the issue of choosing to use the nuclear weapons as an effective means of ending the war with the Japanese, hopefully covering the morality of war and choices/decisions that must be made in such times.
To start, and in immediate counter of the line in paragraph 2 of Bombing Mary: "But the U.S. had already crossed a terrifying moral threshold when it accepted the targeting of civilians as a legitimate instrument of warfare", the cities chosen had large military and industrial centers which were the primary target. Since industrial centers support the military, it is logical to attack them. (Note few if any comment on the same morality of targeting 'civilians' in Germany by bombing ball bearing factories, where civilians worked, train yards, ports, torching farms, etc.) One undeniable fact of warfare that we have been involved in since the Civil War is the loss of civilians - noncombatants. Long gone are the days where two forces line up across from each other, and then shoot and charge one another until one side wins.
We entered an era over a century ago of being able to hit targets of interest from some distance accurately. (Discounting siege weapons which have been available as long ago as the Greek empire (catapult, cannon, mortar, trebuchet, etc).) As technology advanced, better weapons have been manufactured. Most fighting in modern conventional warfare is done at long ranges, with bombers, riflemen, tanks, ships, etc. Very little is done in the up-close-and-personal methods used even through the Civil War of attacking people at arm length or less with sabers, knives, butt-strokes, and bayonets. Soldiers are still taught these techniques, as they do occasionally need them (especially in the new, non-conventional warfare we're engaging in now), but in general war is fought between political powers at long ranges, without 'direct' contact.
The conditions in World War II were no different than in any other war, except for the levels of mechanization involved. Lots (even most) people in the various countries involved had no desire to be at war, and wanted to go about their business. They continued to go to work, but instead of producing cars, they built tanks. Food was consumed by the government in feeding the military, with citizens often being relegated to second-class status. Luxuries were not manufactured when those factories and personnel could be used to make useful items for the various war efforts.
Because these factories and employees ('civilians') were making materiel to support the war, they are considered peripheral combatants. They're not out shooting at the other side, but are making the weapons, tools, and supplies the soldiers need to carry about their business. It should also be pointed out that no rational person wants to go to war. No normal soldier desires to be out killing other people. People who do desire war should be strongly critiqued. Ideally wars are only fought to free repressed nations, or in response to an attack by an aggressor nation.
The Japanese and Germans (being the primary forces of aggression) went out of their way to wrongfully acquire land, resources, and power. They attacked nations who could not - or would not - defend themselves adequately. Hitler was on an intense ego trip, viewing himself as the Uniter of Europe, and establishing the Third Reich (seen by many as a reinstitution of the Holy Roman Empire). He was a homicidal megalomaniac, committing atrocities against not only Jews, but many others just because they weren't like him.
The Japanese had been on a power, land, and resource grab for many years before we got involved after their bombing of Pearl Harbor. I know many of you are familiar with the work "The Rape of Nanking". What the Japanese soldiers did, of their own wicked volition, and under orders was indescribably horrible. The way they treated their prisoners was worse than how you would treat a rabid dog. At least with dogs, most people have the common decency to put them down.
The tortures executed by the Nazis and the Japanese during the 1930's and 1940's has gone down in history as among the worst acts committed by man against his fellow man. (Along with Stalin, Pol Pot, Mao Tse Tung, et al.)
The morality of war is only (perhaps) easy to determine after the fact, and occasionally during the fact. The immorality of not acting when you see wicked being done is (with rare exception) far greater than the immorality of trying to stop the aggressors with violence and bloodshed. Romans 13:3-4, "For rulers are not a terror to the good work, but to the evil. And wouldest thou have no fear of the power? Do that which is good, and thou shalt have praise from the same: for he is a minister of God to thee for good. But if thou do that which is evil, be afraid; for he beareth not the sword in vain: for he is a minister of God, an avenger for wrath to him that doeth evil."
In the context of the morality of certain decisions must be looked upon side-by-side with the firebombing of Dresden1 and Tokyo2,3. The entire point was to cause a massive firestorm in the city and burn out everything and everyone in the town. Consider also the case of Coventry4 which was attacked by a massive air strike from the Germans in November 1940. British intelligence, with the great assistance of escaped Polish mathematicians, had broken the German's Enigma enciphering machine, and knew when the attack was scheduled, and almost exactly the forces to be involved. They did not warn the populace to protect the state secret that they could read German communications at will. Tipping their hand that early in the war would have given the Germans enough data to realize their security system was bankrupt, and they would have (most likely) replaced it with something harder to break, and would have probably prolonged the war in Europe more than just the next 4.5 years, maybe even to the point of successfully invading Britain, or causing the 'nuclear option' to be exercised in Europe. An ideal war never has to be fought physically, but can be won through diplomatic channels. Ideally, there would be no wars, but we have been told by Jesus that there will "be wars and rumors of wars" before He returns. One thing we (the United States, and other democratically free nations) have worked very hard to achieve is 'bloodless' war. We sent cruise missiles through downtown Baghdad, following the streets, and making turns, just to hit targets (and to show off a bit) when no one was in the buildings.
However, evil regimes will hide, or shield their militarily significant resources in hospitals, schools, and shopping centers just to make the decisions to hit them and remove them more difficult on our part. The emperor of Japan (through his cabinet5) during WWII did this in Nagasaki and Hiroshima. Saddam Hussein did it for at least 15 years (before, during, and after Gulf 1, through Gulf 2). Adolph Hitler did some of this disguising during WWII, too. As a general rule, it has been only homicidal, egotistic, and/or dictatorial leaders who have done this kind of obfuscation. In general in the West (i.e. us and our allies), we put militarily significant targets a ways away from civilian centers (Washington DC just happens to be a civilian center, in truth it's a militarily interesting target). There is always the possibility that civilians will be near military targets, but those that are tend to be of the 'interesting' type.
Also bear in mind the very probable realities that would have faced us if we had had to attack Japan in the 'conventional' fashion, including an eventual invasion with ground forces. Considering the losses we sustained at Iwo Jima (>26,0006, with a total of ~70,000 invading US troops), compared to the ~27,000 Japanese on the island (who suffered near 100% casualties), it is very likely that an invasion of Japan's homeland would have consumed the United State's military for an additional 1-3 years (conservatively), and would have amounted to 50-90% casualties of Japanese citizens (yes, citizens who would be defending their homeland, and therefore be soldiers) and US casualties estimated in the mid-100 thousands to possibly a million lost US lives.
In the context of what was likely, based on current (and even, in retrospect, far newer information), sending the two bombers to deliver the atomic bombs 'Fat Man' and 'Little Boy' was reasonable, carefully considered (for a long time, by lots of people, with lots of opposition7). President Truman ordered the bombs to be used on military targets, and intelligence available then (and since) has shown both of these cities to be predominantly military targets. (Also note that 2 more cities were on the schedule to be attacked, had Japan not surrendered.)
The BreakPoint article I'm responding to does make the point that a lot of civilians, and especially Christians, were killed in the attacks. I'm sure lots of Christians were killed who were members of the German, Italian, Russian, British, and American armies. There were probably even some Christians in the Japanese army, who were fighting for what they believed in, or what they had been forced to do.
I think the real point of the article should have been the morality of war. Not the relative strengths and weaknesses of certain decisions. When is it right to kill other members of God's special creation who bear His likeness? There are direct cases in the Bible wherein the destruction of certain nations, cities, and individuals was ordered by God (lots of it in Joshua), which would seem to make it right in those cases. Capital punishment for crimes worthy of death has been directed by God as early as the Noahic covenant (Genesis 9:5-6: "And surely your blood, the blood of your lives, will I require; At the hand of every beast will I require it. And at the hand of man, even at the hand of every man's brother, will I require the life of man. Whoso sheddeth man's blood, by man shall his blood be shed: For in the image of God made He man."), and repeated many other times in the scriptures.
Most often, certain decisions made in times of war are made, not because of their inherent 'rightness' or morality, but because to not do them would be a far worse crime. The question could be asked, "Would it have been better if the US stayed out of the war entirely?" Certainly we sacrificed many thousands of lives in that effort. Should we even be defending ourselves? If it is God's place to take vengeance, why not just let anyone roll over us, stomp us into the ground, and wait for God to take care of the problem?
We fight because it is our duty to protect the "widow and fatherless", to uphold justice to best of our ability in this life. God has called us to be citizens of a different city, the Kingdom of Heaven. But while we're sojourners in the earth, we're supposed to be trying to bring as many people with us to the new city as we can. Sometimes the aspect of "recruiting new citizens" involves stopping the unrecruitable. Sometimes stopping them requires their death.
I look forward to meeting those pulled from this world in those bombings in heaven, just as I look forward to meeting other martyrs, just as I look forward to meeting those who just died peacefully in their sleep. "It is appointed once for man to die, then comes the judgment" [Hebrews 9:27]. Those who have been called in Christ died with Him on the cross, and their judgment has been issued already: Not Guilty. Those who are outside of Christ still have their death coming to them, the eternal death and suffering of Hell because their judgment is awaiting them.
George Whitefield said, "We are immortal till our work is done." Their work was done, and God called them out to Himself. Had we not used the two nuclear devices, they would have been called out some other way. We need to rest in the fact that God ordained what has happened, what is happening, and what will happen.
* (http://www.pfm.org/AM/Template.cfm?Section=BreakPoint1&Template=/CM/ContentDisplay.cfm&ContentID=16548 | http://warrenmyers.com/war/Bombing_Mary.pdf)
0 http://www.pfm.org/AM/Template.cfm?Section=BreakPoint1
1 http://www.spartacus.schoolnet.co.uk/2WWdresden.htm
2 http://www.theatlantic.com/doc/prem/200207/rauch
3 http://www.commondreams.org/headlines02/0310-01.htm
4 http://en.wikipedia.org/wiki/Coventry
5 By the 1930s the Japanese cabinet was largely composed of pseudo-fascist military leaders who used the Emperor and his supposed divinity as an ultranationalistic rallying point for expansion of the Empire. When World War II erupted, the Emperor was the symbol soldiers were indoctrinated to fight and die for. (Wikipedia article: http://en.wikipedia.org/wiki/Emperor_of_Japan)
6 http://www.military.com/NewContent/0,13190,NI_Iwo_Jima2,00.html