Egyptian military knows the right muslims to kill.
Muslim brotherhood is trying to kill Egyptian Christians, to rally religious bigots to their side.
In this case, the Egyptian military is doing G-d’s work.
I expect an Egyptian version of the Algerian troubles. Hundreds of thousands dead over a decade would be a conservative body count projection. If I recall my survey data correctly, Egyptians are reputedly way nuttier than Algerians about Islam.