My take would be that if the law was changed to allow a full marriage in church, and it be legally recognised as that, then the church would have to abide by the law

There's a blurring of language there that is crucial. The proposal is that churches that wish can ALLOW full marriages in their building. That's a totally different to the b&b case and how your sentence seems to read, that the law would be churches CANNOT REFUSE full marriages in their building. I'm only uncomfortable with the 'allow' version because I doubt if it is sustainable and will inevitable be changed in time to the 'cannot refuse' version. I think sailgoldie is absolutely right that there is a confusion between the religious and civil aspects, but also that secular society finds it difficult to accept the religious folks believe that there is more to their church building than a pretty location.

I doubt that many secularists would insist that a foolball stadium had to allow a cricket team to play on their pitch just because they wanted to: both sides have rights and sometimes the rights of the owners do take precidence of the rights of the potential users. The question is always how you balance the rights. My personal view view is that any site that wants to allow a wedding to take place should be allowed to, be that church, hotel, historic site or forest glen, but that every site should have the right to decline to hold such a service, be that church, hotel, etc, etc.