Timeline of 1945:
- Feb - firebombing of Dresden
- Feb/Mar - battle of Iwo Jima
- Apr 12 - Truman becomes president.
- May 30 - Groves and Stimson begin to butt heads over targeting Kyoto.
- Jun 16 - committee rejects a demonstration bombing
- Jul 16 - Trinity test
- Jul 25 - Truman's diary entry
- Jul 30 - torpedoing of the Indianapolis
- Aug 6 - Hiroshima bombing
The Allies started out by trying to use precision bombing against Germany, but they found this difficult to do, so they changed to carpet bombing. This set a precedent and put military brass and politicians in a mind-set where there was no longer any real pretense of trying to spare civilian lives. The Battle of Iwo Jima convinced military planners that an invasion of the Japanese homeland would be incredibly costly. Against this backdrop, there was irresistible momentum for using the two available bombs on one or more Japanese cities, and opponents like Szilard were sidelined.
When Truman became president, he knew nothing about the bomb and had to have it explained to him. He was not closely involved in targeting decisions. The main people involved were General Groves and Secretary of War Stimson, who was 77 years old. A committee began discussing targeting on May 30, which was before the Trinity test. At this point, the explosive yield of the bomb was highly uncertain. There was a betting pool (Rhodes, p. 656) among six of the top physicists as to the yield of the Trinity test, with people betting on figures of 0, 0.3, 1.4, 8, 18, and 45 kilotons. This meant that while the targeting decisions were being made initially, there was so little knowledge that nobody could actually project civilian versus military casualties, or the effect to be produced by dropping the bomb in one spot versus another.
The torpedoing of the Indianapolis, with men dying horrible deaths in shark-infested waters, hardened attitudes toward the Japanese. A committee had rejected a demonstration bombing, which was associated with the idea of putting bombs under international control. These hardening attitudes were to some extent vindicated after the Hiroshima bombing, when George Marshall was shocked to find that one bomb hadn't even been sufficient to convince the Japanese to surrender unconditionally (Rhodes, p. 736).
The debate over targeting Kyoto
Before FDR's death, Groves and Stimson began an ongoing battle as to whether to target Kyoto. Stimson wanted to preserve the historic city, for reasons that continue to be debated, while Groves wanted to target it. This battle went on for a long time, so basically any possible debate as to military versus civilian targets never really happened, because it was diverted into this channel. Truman seems to have been involved in the whole targeting discussion only because Stimson kept invoking Truman's support in Stimson's pet cause of not targeting Kyoto.
The criteria used for targeting do not really appear to have included any consideration of Japanese civilian deaths. They were concerned with not killing American POWs (there were none in Hiroshima) and with using targets that had not yet been hit by conventional bombing -- a pristine target would make it easier to determine afterwards what the nuclear bomb's effect had been.
Reading Rhodes, I felt confused about why Stimson didn't want to bomb Kyoto. Wellerstein has an interesting discussion of this, and seems to indicate that historians are puzzled by this as well. Stimson had visited the city during the US occupation of the Phillipines, and may have gone there on his honeymoon. Kyoto had historical and religious significance (Wallerstein, Kelly, Malloy). Kyoto was a tempting military-industrial target (hence Groves's desire to target it), but according to Kelly's analysis Stimson probably wanted to spare the city in order to minimize Japanese anger and resistance, which he believed would be excited by the destruction of a historical and religious site. Malloy seems to agree with this, citing a couple of relevant lines from Groves's autobiography.
There is clear evidence, from after Hiroshima, for a picture of Truman's feelings of guilt, emotional dissembling, and lack of understanding of the technical issues. Oppenheimer and Truman met for the first time on Oct. 25, 1945. My info on this meeting is from Bird and Sherwin, pp. 331-333. Oppenheimer was shocked by Truman's ignorance when Truman claimed that the Russians would "never" be able to build a bomb. Oppenheimer wrung his hands and said, "Mr. President, I feel I have blood on my hands." Truman became very angry about this. This clearly had hit a sore spot. On the one hand, Truman embellished the story later to make himself come out looking tough. On the other hand, he later muttered to himself about having blood on his own hands. The Bird-Sherwin biography quotes contemporaries' opinions of Truman re the nuclear issue on p. 333: that he was "small-minded" and "a simple man." They summarize these common impressions by saying that "Truman's instincts, particularly in the field of nuclear diplomacy, were neither measured not sound--and sadly, certainly were not up to the challenge the country and the world now faced."
A hypothesis about Truman
So I think the basic story here is that the decision was set on track to bomb one or more cities during a period when Truman didn't know about the bomb, and by the time Truman became president, the debate had already been channeled into a decision between Kyoto and other targets. Little was known yet about the yield of the bomb, and Truman understood even less of the technology. He didn't attempt to question the decisions of people who had already been running the bomb project before he heard about it.
Regardless of how passive, uninformed, and uninvolved he was on the targeting issue, he can't possibly have been ignorant of the fact that Hiroshima was a populated city. His diary entries show that he was at least involved and informed enough to have been conscious of the debate about Kyoto. His diary entry shows a cursory moral struggle with the fact that, given the yield measured in the Trinity test, he would clearly be killing something like 100,000 people. This was probably less a real personal struggle than an attempt at test-driving his propaganda for use after the bomb was dropped. His propaganda (and/or self-propagandizing) made use of absurd rationalizations: that Hiroshima was "purely" a military target, and that by targeting Hiroshima rather than Kyoto they were taking some kind of moral high ground.
A more detailed but more uncertain story-line that seems at least plausible to me is the following. This is supported by Kelly and Malloy. Stimson, an experienced imperialist, wanted to spare Kyoto out of cold-blooded calculation regarding the postwar tractability of Japan as a US dependent. Because of this, he made various cynical and specious arguments to Truman, e.g., exaggerating Kyoto's status as a civilian target and Hiroshima's importance as a military target. Truman was incurious and not very smart, and possessed nothing like Stimson's extensive personal experience in Asia. He took the bait and exaggerated the spurious distinction in his own mind in order to self-propagandize and publicly propagandize about US morality. Because the bombing plan had been a long time in the building and had such momentum, it would have taken tremendous moral and intellectual authority, energy, and self-assurance to turn it aside in any significant way. Truman did not have those qualities in such exceptional quantities. However, he did have the moral qualms about mass killing that any non-psychopath would have had, so he needed rationalizations. Stimson gave him one.
In support of this interpretation, it appears that professional historians have also seriously considered the hypothesis that the decision makers were "self-deluded." See Kelly describing Sherry's opinion of Stimson.
Rhodes, The making of the atomic bomb
Bird and Sherwin, American Prometheus: The trumph and tragedy of J. Robert Oppenheimer
Jason M. Kelly, “Why Did Henry Stimson Spare Kyoto from the Bomb?: Confusion in Postwar Historiography,” Journal of American-East Asian Relations 19 (2012), 183-203
Sean Malloy, “Four Days in May: Henry L. Stimson and the Decision to Use the Atomic Bomb,” The Asia Pacific Journal, Vol. 14-2-09, April 4, 2009.
Alex Wellerstein, "The Kyoto misconception," http://blog.nuclearsecrecy.com/2014/08/08/kyoto-misconception/