Although I don't agree with you, I understand your position. You remind me of the very conservative Catholic who works in my office. He is extremely anti-abortion, anti-suicide, anti-right-to-die, anti-death penalty, and anti-war in all but the most extreme cirumstances, which he is unable to define. He goes to Mass almost every morning and refuses to socialize with anyone who has divorced, and he and his wife home-school their seven kids. He also thinks that the firebombing of Dresson and the dropping of the A-Bombs in Japan were crimes against humanity. I will ask you the same questions I have asked my co-worker: Looking back with the benefit of hind-sight, what would you have done differently to end the war in both Europe and the Pacific? The guy from my office has yet to answer the question. Can you? (Please note that holding hands and singing "Kumbia" is not an option.)
I am not at all making a pacifist argument here: I am not a pacifist, and I would argue against pacifists and say that there is such a thing as a "Just War" and also such a thing as an "Unjust Peace." I would go so far as to say the USA was morally obliged to directly target and destroy as much of Japan's murderous war-making capacity as possible.
However, the killing of civilians was certainly part of the U.S. strategic intention. The shock of seeing an entire city, together with its inhabitants, turned in a moment into a raging inferno, was decided upon in order to break the Japanese will to resist.
Was the bombing of Hiroshima and Nagasaki the only option which could have saved the lives of thousands of US troops, and thousands of Japanese civilians as well, in the short or long run? We can't be sure of that. Using the atomic bomb to destroy a place that had far fewer people but huge psychological value (e.g. the top of Mt. Fuji) might have also saved those lives.
Maybe, maybe not. If we'd done it, we'd have soon found out. But turning an entire city into an Auschwitz crematorium cannot be justified.
Furthermore, in the case of the deliberate targeting of a city as such, together with its inhabitants, the resulting deaths cannot be considered "collateral damage." This is because the deaths were not only foreseen, but intentional.
When we're talking about the direct and deliberate killing of innocent persons, the numbers make no moral difference, and the means are just a technical detail. Whether with abortion, or bullets, or conventional bombs, or a baseball bat, or knives, or nukes, or fueled-up jet airliners on a deliberate collision course --- targeting the innocent is always gravely morally wrong.
This pertains directly to the honor of the soldier; the warrior ethic; and the legitimacy of lethal force.
Without belaboring the motives of President Truman, or Secretaries Byrnes and Stimson in authorizing the dropping of these bombs, we should not forget that Generals Dwight Eisenhower, Douglas MacArthur, Omar Bradley, Curtis LeMay, Henry Arnold, and George Marshall, and Admirals Lewis L. Strauss, Ernest King, and William D. Leahy all opposed the use of these bombs on both the grounds that they were militarily unnecessary as well as morally repugnant.
By the way, it's very much to America's credit that we DON'T practice indiscrimate destruction in places like Iraq. The USA forces (as far as I know) have strained every muscle to protect civilians, even under the most desperate circumstances.
There is detailed, heavily documented book by Gar Alperovitz, The Decision to Use the Atomic Bomb (Vintage Books, 1996), that argues that Japan was ready to surrender, was sending peace offers through the Russians (Russia had not yet declared war on Japan), and needed only the assurance that the emperor would not be tried as a war criminal, as in the event he was not. But Truman refused to change or clarify the demand for "unconditional surrender." Further, Alperovitz says, the U.S. knew that the war could be ended without an invasion of Japan and therefore the argument that the bombing was necessary to force a surrender without an invasion was specious. He says, and lays out a detailed argument, that the real purpose was to end the war before the Russians declared war on Japan, which they had pledged to do by mid-August, and to show the Russians what the bomb could do in order to make them easier to deal with after the war.
If true, this is indefensible.