Well, it's obviously a mess, but.
There is a famous story about a Catholic and a Jew who wanted to get married. The local Priest didn't think Catholic boys should marry Jews, and the local Rabbi certainly didn't think that Jewish girls should marry anyone other than Jews. However, the local Vicar thought that it was his job to marry anyone in his parish who wanted to get married, regardless of their faith, so he married them.
Anyone who ever read the Dandy knows that the longest word in the English language isn't "antidisestablishmentarianism", it's "smiles".
Some Anglican clergy have genuine, sincere, theological beliefs that marriage is something which can only occur between a man and a woman. I realize that territorial battle lines have been drawn, and you either have to see these people as martyrs or homophobes, when they are mostly neither. The point isn't whether they are right, the point is that it's really what they think.
It is very easy to write a law which says "so far as the state is concerned, marriage is now between any two people regardless of sex, but naturally, the Seventh Day Adventists and the Wesleyan Holiness people don't have to marry two men if they don't want to, any more than they have to marry two people who they don't think are sufficiently Wesleyan, sufficiently Holy or sufficiently Adventurous." The state has no interest in what ceremonies are performed by particular sects.
But it is very difficult for the law to say "marriage is now between any two people, but individual clergy of the established church don't have to marry two ladies if they don't want" because the whole point of the established church is that it will marry anybody, christen anybody, and bury anybody who asks them do. (It prefers that the parents of the people it christens so some signs of understanding the Anglican teaching on baptism, and that the people it buries are dead.)
So, as someone with some background in games design, the proposed law which says that any sect is free to conduct same sex weddings if they want to, no sect has to conduct same sex weddings if it doesn't want to, and the established church isn't allowed to even if it does want to is actually a brilliant manoeuvre given that the rules of the game are where they are. If we didn't have establishment, then the situation wouldn't arise, but we do, and we're stuck with it, because Dave and Ed and Nick love basking in the reflected glory of the Queen, and any suggestion that we might change the Queen's job description would be denounced as treason by the people who really run the country (Murdoch and Dacre.)
It's still a mess, though. I still think we should go for the Hamlet option...