Japan raped its way across China and was in league with a nation that wanted to commit genocide on those it deemed impure, alcoholics, addicts and so on.
https://en.wikipedia.org/wiki/Nanking_Massacre
They did horrible things that make the atomic bombs look like vacation. While the civilians were not directly guilty ( they still fed those soldiers, produced their weapons and ensured they had a place to retreat to ) of all those things, they were still what kept the army afloat.
So why exactly is it wrong, in a war against an axis of tyrants and psychopaths, to fight fire with fire? Had the Axis won we'd have seen hundreds of millions killed due to their race. Two atomic bombs are a small price to pay in order to quell that evil for good.
What kind of General could look the wives of his fallen soldiers in the eyes and say
'' We could've ended the war sooner. Your husband would still be alive, had I bombed their cities. But I put the lives of their civilians, the ones that feed the army, above that of my own men. "
Holy hell, I'd see that as treason. As the military leader your main goal is to kill the enemy and protect your own men/nation. And that's precisely what they did.