Here is a great tongue-in-cheek piece on how to neutralize Al-Qaeda from Brant at Letters From Kamp Krusty:
Al-Qaeda is almost impossible to stop. This is, in large part, due to the way its message works, and the way the work gets carried out...
So, in the service of national defense, I propose the following, in order to effectively neutralize the movement. Let's get Al-Qaeda to...
1) Complexify the message
Right now, it's so simple, it can pass from one to the next, and be easily grasped by the uneducated, the young -- everyone. This is dangerous, because it's highly contagious, and people on the street feel capable of enlisting others in the cause.
2) Construct a less "flat", more hierarchical structure
Currently, small, underground groups can move nimbly and autonomously, complicating efforts to thwart them. A more regimented, stratified approach, where some members are left thinking, "I can't know enough to do anything" would bring the movement to a halt.