Well either the government is separate from religion in which case it's legal definition on the rights of marriage theoretically has no bearing on the religious component or it is part of the religion in which case it can decide how it wants it's religion to develop. I can't speak to civil unions in the UK but in New Zealand there were definite rights that were excluded from civil unions (adoption being one) so the argument to have it be recognized as one entity so that distinctions can't be made is a fair one.

As to forcing a church to marry two people I'm torn. I put it in the ball park of refusing to marry those of a different race or have mixed race weddings. I think you can make the argument that any religion that has a form of tax exemption could be required to not discriminate and hold basic human rights. Ofcourse it's a bit of a mire as you could argue back and forth all day between the "state opression of religion" to the "no they can't make human sacrifices" extremes.

As to the mosque/synagogues stuff I'd assume any law that was created would hopefully lead to a lawsuit (from the muslim/jewish/XXX couple or human rights group) which would show that the law did apply to those institutions. But I agree political discussion is generally avoided out of either the fact that they're a smaller part of UK culture or fear of inciting violence(even if this fear is unjustified) or being called a racist(or the theological equivalent (I for one wouldn't like to be called a theist ;) ). I think the "and they are lynching negroes" point is going to be a particularly useful one for the catholics/christians to argue.