Islam and how proposals of religious freedom for the young America would affect Muslims (and other outré non-mainstream-Protestant believers like Jews and Catholics) came up repeatedly during the debates around the Constitution.
Islam was a particularly interesting edge case for discussing religious freedom; there were few (acknowledge) Muslims in the young United States (the faith of some black slaves notwithstanding), and Islam had old connotations from the days of the Crusades and the Reconquista, as well as contemporary connotations of the Barbary states. Muslims were considered about as exotic as could be imagined when it came to discuss the extreme cases of how religious freedom might work.
And, yet, there they were, used by folk like Jefferson, Madison, and others. None of them were particularly enamored of the idea of Muslims taking government offices in the new Republic, but they found the idea of religious freedom even more compelling, seeing the very real and historically present dangers of religious tests and state-sanctioned religious orthodoxy as much greater dangers.
It was an enlightened attitude, and one we should try and bear in mind today when too many folk argue that "Muslim" naturally equates to "Anti-Western Terrorist and Conspirator" and "Islam" isn't an actual religion, and therefore should garner no protection; those very arguments can be similarly used to exclude people of any faith from public office … and have been.
The fascinating history of how Jefferson and other Founding Fathers defended Muslim rights
Thomas Jefferson and others explicitly mentioned Muslims in outlining the parameters of religious freedom and equal protection in the U.S.
