Until the populations of those Muslim dominated societies (essentially theocracies) decide that the rule of law in their land should not be based on a book written centuries ago, the population as a whole will remain at the mercy of the extremists. There will never be equality for women, there will never be religious tolerance, there will never be acceptance of the gay population, etc. While they continue to govern their own populace with outdated, contradictory, racist, sexist, homophobic laws, they will also mold their diplomatic stance in the same manner. This combination of inane religious doctrine along with an extreme lack of tolerance is a breeding ground for those that choose to commit acts of terrorism under the guise of martydom.
If you continue to deny rights as a state to women, other religions, homosexuals, etc all based on religious doctrine, you have given credence and support for the rest of the garbage contained in the "holy" books.
If you base any governmental policy on religious texts (aside from the basic stuff like, generally don't rob or kill people, try and help out the less fortunate) you've got a lot bigger problems than just promoting violence. I haven't read the Koran, and I'm not that well-read in the Bible, but I'm pretty sure you could scour the text and not find all that much input on the best way to promote economic growth, how to design a computer, build roads, figuring out a quality healthcare system, monetary policy, etc. If you think I'm exaggerating, there were a bunch of nutjobs going around in Iraq for a while shutting down ice vendors because ice isn't mentioned in the Koran.