Crusades Redux?

I just finished reading a column on NYTimes.com (registration required) about separationist vs. neutralist viewpoints on the whole church/state fiasco. And it occurred to me, in light of the earlier posting from Foreign Affairs, that part of what makes the US great is that we do allow a total assimilation and appreciation of all cultures and religions. If we pursue the separationist view, do we risk creating an alienated sub-class in our country determined to get their view heard once 43 is out of office?