What do you do with the ones that are already here?
What rights would you allow to US citizens who practice Islam?
You do not give them a visa.
The ones who are here, you ship them out.
US citizens who chose to be Nazis in WWII were hardly tolerated.
They should be shipped out too.
What rights do we allow to US citizens who practice murder?
Not all Muslims seek actively to murder non-Muslims. But all Muslims subscribe to a religion that justifies and even commands as a religious duty (an imperative that trumps the law of the state) the subjugation or murder of non-Muslims.
So what do you do? Nothing? That will probably work, and imperfectly, only so long as Muslims remain a minority in a non-Muslim country.
Stop issuing visas.
What do you do with the ones that are already here?
Cancel their visas and annul any naturalizations.
What rights would you allow to US citizens who practice Islam?
The same as all other US citizens.