Maniac,
" I'm not seeking to prevent any C of E member from doing anything."
You're seeking to force C of E clergy to perform ceremonies that violate their consciences.
"If a church believed in forced marriages would the right to freedom of religion come before a person's right to choose who they marry."
It's a good question. The answer is no, because somebody's right doesn't enable them to force somebody else to do something in violation of their rights -- which is exactly what you're trying to do. So your position is exactly analogous to that of the church in your hypothetical.
"This doesn't mean that I'm not stupid, of course, but it does mean my stupidity is shared by some human rights experts."
No it doesn't. It means you just can't distinguish this case from that, even though there's a distinction.
Mr. McFarlane's employer was in the business of giving sex therapy to couples. His employer, a private organization, felt that he could not perform his job (which was not related to religion) because of his religious objections, so they fired him. Of note, the government here did not force anybody to do anything -- it was a private employer that made its own policy decision.
On the other hand, if a CoE priest were forced, against church beliefs, to perform gay marriages, then it would be interfering directly with a group whose PURPOSE is religious, making their religious leaders act against their own religious beliefs. It would, in short, be the _government_ forcing the pastor, the entire purpose of whose job is to lead religious observance, to violate that religious observance.
So whereas the first case has nothing to do with the government coercing anybody to do anything (against his conscience or otherwise), the second case involves the government coercing a religious organization to violate its own beliefs about its faith and practice. Thus, the first case does not involve government violation of human rights, whereas the second case is all about that.
So, another analogy fail. And please -- don't put your own bad reasoning in the mouths of European human rights experts.