What about 'The Bomb'?

After watching Hitchens, Dawkins and Harris defend atheism against the charges of Stalin, Mao and Hitler I began to wonder about the atomic bomb in Hiroshima and Nagasaki.

The first, and only, country to use atomic weapons was the U.S. Many people in the West are terrified of what will happen if Iran or North Korea get nuclear weapons. The fear is that these countries will use them in a religious war against us. Of course, we all know that those evil Muslims wouldn't think twice about bombing civilians - just look at 9/11!

However, the bombings of Hiroshima and Nagasaki were CIVILIAN targets! Why do we fear Muslims with WMDs when we already know that the U.S. will attack civilians?

The Japanese did a pre-emptive attack at Pearl Harbour; a military target. Certainly a tragic event. But what led the U.S. to bomb two civilian (non-military) targets?

If the U.S. administration were religious was their decision based on religion? Was the attack a 'Christian' attack on the evil 'god-emperor' of Japan?

On the other hand, if the decision by the U.S. were a 'secular' one, why did they attack a (presumably) innocent, civilian population?

I find it interesting that none of the religious debaters ever use the bombings in Japan as an argument against secular states. I presume that they believe the bombings had some sort of religious influence.

On the other hand, the atheist debaters don't mention the bombings either. Is it possible they think the bombing was a poor secular decision?

If anyone has any insight on this I'd really appreciate some input.