First I want to make sure that you understand that my comments are based on a basic disagreement on the Constitutional issues here and not one of trying to validate the legitimacy of the Muslim religion. Those who murder in the name of their faith should face the death penalty. But to round up all members of that faith because some have murdered is, IMHO, against the laws of the land.
Now, having said that, you stated above that Islam is a religion. What Jefferson has written, in private letters or other sources, in regards to this subject, is secondary to this:
Amendment I: Freedom of speech, religion, press, petition and assembly.
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.
I am afraid that winning the war on terrorism is far more complex then simply rounding them up and throwing them out.
This last phrase has not been held to grant license to commit human sacrifice or acts of violence. It purely means that people can believe as they please, and communicate their beliefs without the federal government's interference
Being a member of a terrorist group, contributing funds for terrorism, sheltering terrorist fugitives, and openly advocating terrorism are not protected religious activities