How about we make them lose their faith.
The only way to deal with such fanatics is to show them their faith is false and worthless. We should paradrop 100,000 homosexuals into Mecca and let them have a year long gay pride parade. They can then use the sacred texts of Islam as towels to wipe up the mess of their fornicating. After Muslims see how Allah does nothing to the perverters of the holy city, maybe they'll get a clue. If not, we can always nuke it.