I cannot imagine that a homosexual couple would actually want to be married in a church that believed strongly enough that it was wrong that it would object to them choosing it.

Oh, I can. There are all sorts of folks, including those who would do that because it is an important point of principle. And I could imagine a protest group outside a church that refused gay weddings but allowed hetrosexual marriages. And wouldn't that make the straight couple's day? And what resentment might that trigger? As I say, handled badly this could be very divisive.

I imagine that if this or similar legislation occured some churches (such as RC) would adopt saulgoldie's approach - which is, I think, what happens in France - that the church weddings would drop all civil aspects for all weddings, so that there is registrar for example. This would be followed by a completely separate civil ceremony at the registry office