Ron Bailey has been reporting on the conference in Orlando, and this post includes a lengthy discussion of my talk.
One point of disagreement is about the contraceptive mandate, but at least as far as the Letter Concerning Toleration is concerned I still think I am right. It's possible that Locke would have been opposed to the law in its entirety, thinking it is not in the public interest to provide government-mandated insurance cover for contraceptives, and such a law should not be enacted at all. But assuming the law was duly enacted and especially if it was justified on secular grounds, Locke's official position would seem to be "no exemption for Catholic employers" - he was generally and straightforwardly opposed to religious exemptions from secular laws. That was the question I took myself to be dealing with.
In Freedom of Religion and the Secular State I do discuss reasons why, in the twenty-first century, given developments over the last 150 years in the kinds of laws that get enacted, we might take a softer line and allow some religious exemptions. We don't have to follow Locke's reasoning all the way through on every point, and perhaps he would change some it if he saw the modern welfare state in action. But I think that's a further question that we didn't get to in Orlando (again, I certainly do get to this sort of question in the book).