Interesting. TK, I give you credit for having pluck. However, your sense of history is skewed. I also can't help but wonder how on the one hand you seem to intimate that if you don't want to get hurt you don't go to war, but then seem to scream when the pain is applied. The sad fact is that no matter what kind of bombing you did in Japan, many people would have died b/c of the density of the population. It's only about the size of California and had a population of around 75-90 million or so at that time. It's a fact that more people died in the fire bombings of Tokyo than in Hiroshima and Nagasaki. War is ugly and it's debatable in total war just how innocent civilians really are. Japan was mobilized across the age spectrum, so many people were little more than REMFs in the war effort (that would have been more or less true in the allied countries as well). Is the real upset from the fact that so many people died in the bombings or is it the nature of the bombs themselves that really disturb you?
As to the opinions of people like Eisenhower and Nimitz, they were only that. Both men realized that Japan was defeated in the field, but that did not mean that they were ready to surrender. It literally took two A bombs to force the emperor's hand to press the military government to finally cave and accept surrender. Even as Japan was going down on the mat, they still were prepared to inflict ugly losses on any operation mounted by the allies. The Americans found many hidden suicide weapons throughout Japan after the surrender. Had Hirohito demanded their lives, they'dve gladly died. Battles like Okinawa, with over 150000 Japanese casualties and something like 37000 US dead and wounded were an omen of how costly an invasion would have proven. On top of which, had we merely embargoed/blockaded Japan, a larger number of civilians would have perished from starvation and other diseases. The atomic bombings were basically the better of two bad choices. As ED basically pointed out, once the enemy has accepted his defeat, THEN the healing and rebuilding can begin.
As to your contention about NY and Iran, that begs a question. Has the US attacked Iran first militarily with nukes? If so, the Iranians would have the right to strike back with whatever they could. Would it be wise for them to do so? No. Simply because we would turn Iran into a liquid glass cauldron. If Iran were to launch a nuclear Pearl Harbor vs NY, then that would not only be wrong, but foolish as well for the reason already stated.
What is the bigger atrocity in war: to strike with a weapon so horrible as to end a conflict or to drag out the struggle, killing many more people, such that you can claim some kind of moral highground?
Chances are that had the Emperor in fact had a big enough set to force his military leadership to surrender sooner, he could've spared his people greater suffering. You can't start a war and then try to sue for favorable terms b/c you don't like that you've lost. The world just doesn't work that way.