What's funny is that in the episode "Logical Insanity," he actually does lay out the case for justification of the nukes being dropped. The whole episode is about the insane logic (hence the title) that people use to justify ever increasing atrocities during war, such as the firebombing of Tokyo. The logic being that making the war worse for civilians to bear will eventually lead to them demanding the government surrender, leading to more and more indiscriminate bombing when their government inevitably doesn't surrender. This was back during the era where just about every military higher-up was of the opinion that people could be bombed into submission, because "Why would people just let that happen to them?" I guess.

And he also covers it from the Japanese point of view a bit, as well, mentioning that a significant portion of the Japanese civilian population was ready, willing, and able to fight, and die for their Emperor. In fact, in the newest series "Supernova in the East", he mentions that guy that hid in the Philippine jungle for however many years refused to believe that the war was over and Japan still existed. In his mind, if the war was over, Japan couldn't have existed, because they would have forced the Allies to invade and kill them all.

I'm not saying that the bombings were right in any way, but you can't say that there wasn't justification. The justification was not having to invade the Japanese Home Islands, which almost certainly would have been far worse, both in terms of absolute casualties, as well as in terms of purely civilian deaths. And in the end, the two bombs being dropped was probably the only time in history that the logical insanity actually worked itself out and directly led to surrender as a consequence. But I suppose we'll never truly know, and we just have to live with it.