Both cities were centers for the war industry.
This is true. I have seen lists of military targets in both cities, and they didn't look insignificant to me.
Focusing on the destruction of these miltary targets would have been morally justified -- yes, even if there was quite a bit of honestly "collateral" damage. I would go so far as to say the USA was morally obliged to destroy as much of Japan's war-making capacity as possible.
However, the killing of civilians was certainly part of the U.S. strategic intention. The shock of seeing an entire city, together with its inhabitants, turned in a moment into a raging inferno, was decided upon in order to break the Japanese will to resist.
The number of casualties isn't what makes it murder. The choice of weapons (conventional or atomic) isn't what makes it murder. It's the fact that the decision-makers decided to indiscriminately kill civilians as a means to an end.
By the way, it's very much to America's credit that we DON'T do that in places like Iraq. The USA forces (as far as I know) have strained every muscle to protect civilians, even under the most desperate circumstances.
That's what constitutes the one of the main differences between the USA and the Islamo-fascists. I'd like to keep that distinction clear.