There was not a single Muslim alive in the USA when that passage you quote was written, and it is highly dubious as a matter of constitutional law that it protects Islam or any other religion not in existence in the USA at that time. IMHO it protects only Christianity whether Roman, Greek, or Protestant, and Judaism.
As much as I may wish for the above situation, I can't find that the Constitution applies only to the thoughts that existed in America in 1787. If this were truly the case, then the Internet would not be protected by the free speech clause (chuckle if you're a cynic :) ).
The Constitution may protect a thousand things, including gun ownership [yes, I AM chuckling]...
but not as RELIGION. As Religion, only Judaism and Christianity are protected.
The first Muslim settlement in the US was built in 1790, there were Muslims accompanying the Spanish explorers of the New World since the early 1500's.