I'm fairly certain the soldiers fighting weren't exactly Nazis themselves or believed in the Nazi ideology, but just soldiers fighting for what they're country had interest in and defending it from invasion. SS officers and the government officials however, they were the Nazis who pulled the strings on the holocaust and other evil-doings.

Also the bombings were the lesser evil in terms of causalities, if an Allied invasion had taken place, more than 14.5 million people would've died compared to ~246,000 that did die. Japan was given several warnings and a final ultimatum (All ignored) and millions of leaflets warning the citizens of the bombing were dropped on the target cities, which the government declared illegal to own one/listen to. And Germany didn't nuke Japan because they were allies, Japanese people were considered Aryan by Nazi ideology, and the German atomic bomb program was shutdown before it could be finished.

One more thing, the Japanese aren't as innocent as you think they were in WWII.