My father was in the RAF during WW2 (not in Bomber Command though) and I've often wondered about the morality of what our country did then - the best defense I've seen of the strategy was that unlike for the Nazis the indiscriminate killing of civilians was never a goal in itself for the Allies but something that was a means to the end of finishing the war.

Note that although that's probably the best argument, I'm still not completely satisfied with it.