It specifically allows homeland security to "prioritize" refugees of the minority religions in these countries, which are Christianity and Judaism. Yes, it discriminates based on religion. No way around that.
That may be, however they aren't protected by our laws so it doesn't apply.
if they are immigrating here then it is fair to say that they are trying to come here, yes?
You aren't listening to what I'm saying. If they are here, illegally or not, they are protected, if they aren't here and never were, they aren't protected.