I have heard that most were in support but others expressed disagreement. I have also heard that those expressing disagreement only did so afterward to help their reputations. What’s the real story here?
You have the chronology a bit reversed here, which isn't surprising -- most people are taught this view of the bombings, but it's incorrect. Truman never made a decision to drop the bombs in the way it's often portrayed -- this is a narrative from the postwar period. He made a decision to stop bombings without his express consent after Nagasaki, because he was uneasy about destroying entire cities (it is not clear whether he understood Hiroshima to be a city, rather than a military base). Lots in our FAQ about this, mostly via /u/restricteddata :https://www.reddit.com/r/AskHistorians/wiki/faq/militaryhistory/wwii/usa#wiki_the_atomic_bombs.2C_aka_questions_.2Fu.2Frestricteddata_has_answered
Specifically:
https://www.reddit.com/r/AskHistorians/comments/c34bcf/did_the_atomic_bombings_in_japan_indirectly/
There were several military leaders (of the few who were aware of the atomic bombing plans) who after-the-fact expressed doubts about the utility and necessity of the atomic bombings (which as /u/jschooltiger notes was not something that was really characterized by "Truman's decision," but was something that was discussed among the top generals and admirals toward the end of the war). The most notable of these are Admiral Leahy, Admiral King, and General Eisenhower (and similar attitudes have been attributed to LeMay and Nimitz). It is not clear that any of them actually voiced this at the time, though that does not mean they didn't have feelings about this at the time.
There are two things that make this sort of thing murky to sort out. One is the that after-the-fact memories for things like this are notoriously unreliable. (This affects everyone, not just these generals.) It's easy to make an argument that Japan was on the brink of surrender after they have surrendered; it's harder to make that when they haven't. This sort of post-hoc awareness can amplify nascent feelings and make one remember them as being more strong than they were (confirmation bias). This perhaps explains why none of those who claimed to have disagreed with the use of the atomic bombs never said anything at the time: maybe they felt that way, but they didn't have the conviction to bring it up. (There are very few people who expressed real reservation about the use of the atomic bombs prior to their use, and most of them were scientists involved in the making of the weapons, and those reservations were not passed up the chain of command.)
Second, there is the role of what voicing this disagreement did for them in the 1940s, when these accounts came out. There were grave fears in the US military that the atomic bomb would be interpreted as having been the winner of the Pacific War, and that the extreme hardship undertaken by the conventional forces would be overlooked. Furthermore it was feared that the atomic bomb would be taken as an excuse to cut back on conventional military forces — and that was, as aside, exactly what Secretary of Defense Louis Johnson attempted to do in the postwar. So downplaying the importance of the atomic bomb was clearly for some military figures in the postwar a way to reclaim a perceive lost glory, and to make an argument for a large conventional military. (After the detection of the Soviet atomic detonation in 1949, and with the Korean War starting a year later, the calls to cut the military essentially vanished, and the military leaders quickly made their peace with atomic weapons.)
It doesn't have to be an either/or thing — again, it could be a small feeling that memory and circumstance allowed them (perhaps earnestly, in their own minds) to amplify into a larger feeling in the postwar. The relevance of this, in my mind, is not that we should think, "oh, even the military thought it was unnecessary, so it was unnecessary" — one can make an argument about the necessity or lack thereof of the atomic bombs without this, and it isn't clear this really supports that — but more of an issue of how atomic politics in the postwar was framed in ways that we would find somewhat surprising today (with the military being one of the biggest critics of Hiroshima and Nagasaki, as opposed to its modern associations as a defender of the bombings). I like to bring this up with students just to shake them up from their presupposition that the mapping of political positions onto one's views of the bombings is a tricky one, and one that has changed over time.
Barton Bernstein has written a very nice piece on Eisenhower ("Ike and Hiroshima: Did he oppose it?"), and he also talks about these claims a bit in his omnibus essay, "Understanding the Atomic Bomb and the Japanese Surrender: Missed Opportunities, Little-Known Near Disasters, and Modern Memory," Diplomatic History 19, no. 2 (Spring 1995), 227-273.