It won't take genocide to win the war. It will take a lot of deaths, but considering they want to wipe out everyone who doesn't follow islam, we should at least acknowledge the stakes.
There are secular muslims. Just like there's secular people in every religion and society. There are cultural muslims just like there are those who put up Christmas trees and talk about Easter bunnies but don't go to church every Sunday. Not everyone in muslim countries is convinced they should slaughter the infidels as their prophet commands. The problem is, those secular muslims are terrified of the practicing muslims, and for good reason. You don't dare speak out against jihad, call yourself an atheist, or suggest that maybe mohammed wasn't right about absolutely everything.
So long as we can prevent nuclear weapons from falling into the hands of the fundamentalists, I'm actually pretty optimistic that this war can be won with a minimum of bloodshed (and by minimum, I think back to the minimum of bloodshed it took to defeat fascism or communism in the last century). The world is becoming more and more interconnected. I certainly believe that, given a real choice, everyone would rather live in a westernized democracy than a fundamentalist theocracy where you can be executed for your beliefs or speaking your mind. The more they know about us, the more they will want to be like us. It's just a matter of getting our message, our ideology, out there for people to hear it.
But, in the meantime, we do need to wage the war that they declared on us. We need to do so with all the tools at our disposal, recognizing that there are, indeed, secular and cultural muslims that would support our ideology if given the opportunity to do so, and can be allies against the fundamentalists in the long term. Killing those individuals would be a mistake. But don't for a second think a lot of those individuals are hanging out with terrorist leaders.