Both Chriostian extremists and Muslim extremists are a p[roblem. But they are a minority. I expect that an 80% rule applies -- 80% of the turmoil is genrated by 20% of the people.
Organizations like the al Qeda, no matter how populous, tend to wither away when their drivers are gone. They build their numbers out of people who need someone other than themselves to blame for their own lack of spirit, rather than poeple who are genuinely motivated to forward their cult. Without a ringleader, the vassals disperse to other things.
I believe the vast majority of Muslims in the world would be quite happy to live lives of simple production, learning the peaceful side of the Koran and getting along with others. The fanatacism is a special aberration that really has to be pushed to be kept going.
SO the answer to "what to do" is to (a) constrain those who would resort to violence (b) remove the incentive toward violence by seeking to establish genuine communication and a reaosnable degree of justice and (c) help build self-genrating economic communities.