I was just reading last night that after the Nagasaki bombing, Truman (who hadn't really been involved in the day-to-day planning of the attack) reacted by taking back control of nuclear weapons from the military because he was horrified at how many civilians a single attack had killed. You can criticize him for reacting that way when he was okay with the firebombing of Tokyo (100,000 dead), but I think one of the main messages of all of this is that war is always terrible and there is no way to make it clean.

I really recommend Japan at War: An Oral History for a great, nuanced view of the war from the Japanese perspective. It's got bits from housewives, businessmen, a dance instructor, convicted war criminals, former soldiers, a kamikaze pilot who survived three missions...