Except 90% of Muslims are homophobic, anti-Semitic, and misogynistic and there is no other link than the ideology of Islam.
Islam is an ideology just like any other and a particularly vile one at that and the US has a long history of ideological standards for immigration.
The 1st amendment doesn't apply to immigration and naturalization legislation. In United States ex rel. Turner v. Williams the SCOTUS ruled that Congress "possesses the plenary power to exclude aliens on whatever ground [it] deems fit."
I just finished reading ALL of Turner v. Williams, it does not contain your quote... Maybe I missed it, do you mind citing to a page number?