First of all the bishop of York as an example said on gay marriage that he answers to a higher authority. Rather sinister don't you think?

Silly, yes. I certainly don't agree with his conviction. But sinister? No, not really.

I am not sure exactly what the point of the EU case you referred to is. As far as I understand the legislation, there is explicit provision for the Church of England to refuse gay marriages, but there is no such provision for any other church. So to the best of my knowledge, the Catholic church could be sued for refusing without involving the EU at all, at least at the first step. If the church lost, then certainly the EU would become involved due the arguments about religious versus other freedoms, but that would be a long way down the road.

Where the EU ruling might come into play is whether one church can be singled out for special treatment in law in that way.