Perhaps I'm misreading you -- but are you really saying you think that the current "clash of civilizations" is actually about religion, driven by religion, motivated by religion -- that aggression (on 'our' side) or resistance (on 'theirs') really has its sources in people's beliefs about God?
No doubt people are very good at finding religious justifications to do whatever they want to do anyway. 'Twas ever thus. They can also find excellent Enlightenment justifications if they wish -- making the world safe for democracy or free markets or women's liberation or gay marriage or whatever. The capacity for hypocrisy and flattering self-representation is, it would seem, essentially human and is not, alas, lost as easily as a rosary or a yarmulke.