The Muslim brotherhood was working within a political structure without real power(they were thrown out by a military coup).
As long as they were involved in a legitimate political process they were essentially defanged. I would bet that many members who were not "Radicalized" have become so after the military killed 600+ civilians yesterday alone.
The fact that El Baradei, a Nobel Laureate, liberal, and western favorite who supported the overthrowing of Morsi, resigned his post as Interim Vice-President is proof that things have gotten out of hand with the military.
I think that the internet has sparked some new thinking in Egypt. Used to be, the Egyptian military was in the US pocket, but now they are going against Obama because the information is just all over about how the Muslim Brotherhood is actually a fascist western-based "asset" being used to foment war in the region, and they've decided to put an end to it.