It's a tricky one, Sherman. Purely from a hypothetical viewpoint (and what other viewpoint can there be on this subject?), perhaps God rules upon cases individually, depending on whose side he's on in any particular war. After all, he commands us not to kill, but he's a mass murderer, so by saying 'thou shalt not kill', does he really mean 'do as I say, not as I do', or does he mean that killing people is fine if he is on our side? In the case of Japan, since the Japanese aren't Jews or Christians, he was clearly on our side - so that's alright then - isn't it? :o)
(Incidentally, I'm not really smiling. Nuking Japan, or anyone else, is nothing to smile about - but this is a hypothetical question).