The claim that the history of Europe from 1517 to 1648 shows that mixing politics and religion leads to endless violence, so that peace requires the secular state, always seemed odd to me. After all, states kill by nature, and they can be defended only if someone is willing to put his life on the line. It follows that any state whatever is based on some principle thought worth killing and dying for. Political principles have to do with the use of force to achieve practical objectives, while religious principles relate more essentially to other things. The latter put all practical goals in a larger perspective and so tend to make them seem less absolute. So it seems that the usual effect of excluding all religious principle from public life, leaving only warring political principles, would be to make political conflicts more absolute and therefore bloody. The history of the last century seems to bear that out.
Here’s an interesting account of the “Wars of Religion” and the rise of the modern state that goes into some of the historical issues. The basic claim is that the “Wars of Religion,” which liberals claim led to the modern state as an escape from religious violence, were in fact the Wars of the Rise of the Modern State, which likes and makes use of religious conflict because such conflict advances its project of doing away with independent religious authority and making itself absolute. I think the argument needs clarification, but the piece touches on a lot of material and what’s there is very useful already.