I think you have made a good, reasoned argument.
I just have one important point of caution for you on this statement: "The two atomic bombings killed a quarter million people. On its own, that's horrifying. In the context of the Second World War, that's a rounding error."
While relativity is important in a great many things, it is problematic to use from an ethical point of view. Many atrocities were committed by all sides in WW2. In fact, all sides committed mass atrocities of some kind or another: the fire bombings being particularly awful. This was the reality of WW2 and has given terrible clarity to the reality of what "total war" means.
My point here is simply this: the atomic bombings of Japan were absolutely horrific tragedies. It is an event that stands alone in human history when so many civilians have been killed in an instant. It stands in rare company by the magnitude of civilians that slowly died a truly barbaric death in the hours following. I don't think it is possible to ethically justify total war, and by consequence, no substantive part of it. Thus, while total war was necessary for all sides to wage, all sides had to take unethical actions. I think we would agree on this point: that being ethical in total war would be self-defeating in fact: it would completely ignore the reality of what total war is. This is, simply, where I think people get mixed up about the bombings. They happened because it was total war. But they were not a rounding error on any scale: they were an awful event in our human history that we can only hope is never emulated.