Henry Stimson, the Secretary of War, removed Kyoto as the #1 atomic bomb target because he thought that it's destruction would increase the likelihood that Japan would be driven into Russia's arms after the war. In other words, the decision not to vaporize Kyoto was realpolitik.
I have no such concerns regarding the Muslims.
Hmm, lets see, bomb mecca, and send a 1 billion muslims to the chicomms.
Real smart strategery there.