I have always had considerable difficulty with the idea of directly targeting non-combatants in wartime. But you make an excellent point, one that suggests the moral ambiguity of the situation: Would it really have been better if we had waited to have our own civilians annihilated en masse?
And, as others have pointed out, Imperial Japan's hands were hardly clean, from the bombing of Pearl Harbor to the rape of Nanking.
That said, I am still not entirely comfortable with the thought of our incinerating innocents, even in the service of a larger (and righteous) cause. But would even more innocents have been killed in years of house-to-house fighting? Dunno. Once again, this strongly suggests the moral ambiguity of the situation.
In the end, it was essential to the free world that the Axis powers (including Japan) should be defeated. Even Japan itself has benefited enormously from the post-war transition to a Western-style democracy.
It is just hard to have anything other than mixed feelings about the bombing of civilians--even if the phrase "an inexcusable crime" is clearly hyperbolic.
We fought our way from island to island and the resistance just got fiercer the closer we came to Japan. We suffered heavy casualties on Okinawa. Everything we knew at that time pointed to a horrendously bloody fight if we had to conquer the main islands by invasion.
It could have been much worse for Japan.