This issue is one of the few where I'll admit I tend to vacillate. On the one hand, I certainly understand that most muslims are as non-violent and peaceful as most other people of whatever faith or non-faith. Moreover, I also understand that a relatively small number of very brave Muslims have taken strong public stands against the violence that's been perpetrated in their name, very many of whom are women. I would want to extend the same kind of tolerance toward the first group that I would to any other modes of belief, and I have great respect and admiration toward the second group. But on the other hand, I understand very clearly that what requires such bravery on the part of those who stand against Islamist violence is precisely the extraordinary willingness of a significant minority of Muslims to resort to the most brutal slaughter; I understand how that willingness creates a fear that permeates the culture of the modern world, as we've seen in numerous instances of self-censorship in anything to do with Islam, skewing the treatment of that one belief system alone; and I understand that the minority of Muslims willing to engage in actual violence is supplemented by much larger numbers around the world who sympathize with them in whole or in part. I understand, in other words -- as many simple-minded and self-deluding liberals do not -- that we really are at war with a global ideology, however unusual that war may be by historical standards.
So, given that, here are some tentative generalizations: first, wartime conditions justify -- and often enough require -- restrictions or actions that wouldn't be justifiable at all otherwise. And second, the ideological component of this struggle needs to be recognized and managed -- but we shouldn't be complacent that, in the fight with this particular enemy, our notion of civil rights and religious tolerance will be seen as a strength rather than a sign of decadent weakness. In the end, then, I come down on the side of those who say we should recognize the constitutional right of the mosque proponents to go ahead, but that we should make every effort to persuade/pressure them not to do so. This is a position shared by at least some moderate Muslims too, as this article indicates: "Ground Zero Mosque Splits Muslims", and they'll need the support of non-Muslims so they're not further isolated.