Japan was not all but defeated at the time. It still had the capability to mount a serious, if doomed, defense of its home islands. Whether that justifies Hiroshima and Nagasaki is a different question. Nor do I see how the subsequent occupation changes whether it was a war of self defense, nor whether it was justified.

In Europe, if you're referring to the fact that the primary burden of defeating the Nazis rested on the Soviets - I'm perfectly aware of that. And believe it or not, in spite of being Polish, I think that they were fighting a war of self-defense. Neither the long term occupations of foe and ally alike, nor what happened to the German civilian population  change that.

On the Civil War - well I'll assume you don't care about the fate of Americans, so just think of that of Mexico, the islands, etc.