1. The protection that LE would have to provide for these communities would further drain resources, which means other parts of the city would be less protected.
2. Bin Laden wants an Islamic vs. Christianity/Jewish war, in order to enlist all of Islam to his cause. If you enrage the population to a point where the loose screws are taking potshots at ME people, then we will be playing into bin Laden's scenario, and we might also lose some of those reluctant allies we now have and need, due to their location in the region.