We should kick chaplains out of the military.
Or so James Madison said (as reported by Christopher Hitchens.) It is hard to get around the fact that chaplains are spokespeople for religion being paid by taxpayers' money. But should we deny soldiers whatever comfort they might get from talking to a chaplain or attending a religious service because of a church-and-state debate? That seems backwards. Sometimes the pragmatic concern outweighs the ideological one, and Hitchens is too caught up in the false piety of his own position to consider the effect this would have on soldiers.
He does, however, bring up an interesting point. If the military provides chaplains and/or religious services for every major religion represented, what about Muslim services that would be segregated by gender? When religious teachings interfere with military protocol or standards, the situation becomes much less clear.