Islam has to be denied religious status, and acknowledged as an enemy terrorist organization at war with America. Then Muslim citizens can be arrested and jailed or deported, just as American Nazis could be during WWII.
It can be done. There is no way "religion" was meant to mean a protected belief system that teaches the murder of non-members by the first amendment. No. Way.
The idea that you can exclude American citizens because of their religion alone is clearly repugnant to the Constitution. If you can show a conspiracy or if you can show some overt act such as serving in the Army of a foreign power like Isis, you can probably constitutionally deny that citizen his normal rights.
It is not even clear that you can deny immigration to a class of noncitizens based on religion alone. God knows how the Supreme Court would rule, it is possible of they would look of the fourteenth amendment granting equal protection to "persons" and declare the practice unconstitutional. But one thing is very clear, you simply cannot deprive American citizens of their rights simply because they adhere to a religion.