You're conflating the moral questions with the legal one which Elagabalus referenced.

Do I recognize the freedom of conscience for A to conclude that killing all Muslims is okay?

Of course, we all have free will.

Do I believe that precludes the State from passing laws against killing all Muslims and if A acts upon her or his conclusion to apprehend, try, and punish him or her?

Nope.

A "moratorium on all Muslims entering the country" is a legal issue insofar as "religious freedom" is relevant.