FWIW, these kinds of discussion are often framed in the context of immigration - letting the Muslims in - Clinton has already brought it up. Immigration isn't based on religion, it's based on nationality, and as far as pretty much anywhere is concerned racial discrimination is "any distinction, exclusion, restriction or preference based on race, colour, descent, or national or ethnic origin".
If you've got a problem with Islam, indeed it's not racist, but a lot of the downstream conversation about it is. As soon as your solution to the problem is to stop immigration, it becomes racist.