I am familiar with your point of view. Your opinions are generally held to be true throughout the "enlightened" classes, those folks who respect NPR.
Nonetheless, in war there is no room for sentiment.
A great struggle erupted after the atomic bombings between the "peace" faction, which included sections of the Imperial Navy very impressed with being subjected to a weapon so technically advanced it was as if the bombs were sent from the distant future. This faction carried the day with the Emperor. It looks to me that the Navy would not have weighed in without the bombings, and peace not made.
As is well known the Japanese offered peace early in the year with the condition that the Emperor remain the Emperor, that is, that the existing legal and social order to be preserved in it’s most important aspects. Fortunately this offer was rejected. The Emperor had to reign at the obvious pleasure of the Americans for the thing to work.
Personally I would have sent "fat man" to Kyoto instead of Nagasaki. The Imperial Palace would have been a bad target since Hirohito was needed to make peace, but Kyoto was the ancient seat of the Emperor, the most holy place in Shinto. Been to Kyoto, too. Remarkable historical artifacts, cultural treasures, etc.
I have contemplated the Ryoanji. In Tokyo I have burned incense at the Senkakuji. Those boys had the warrior spirit. Once waited outside the Yasukuni as I did not think a Gaijin should enter.
When wars get out of hand the killing gets manic. This happened in Japan in 1944-45. A traumatic experience for many. That war is sad is no reason to become sentimental over the whole business, though. War is too serious a matter for sentiment, emotionalism, or for fear.
Yes, as I recall Kyoto was not targeted because it was the historical capitol of Japan.