Any time the government has told a group of people to register based on their religion, race, or national origin it has never ended well for those people. Just look at the Japanese internment camps. Sadly Korematsu v. US held that in cases of "emergency and peril" (which is left for Congress to define), the government can exclude and restrict the rights of Americans "to provide for the common defense" and "protect the general welfare". This would allow for any unpopular religion to be targeted for their beliefs.