Churches could limit events to traditional weddings and reject things like dom/sub 'bondings', civil union receptions (even when they aren't legally weddings), plural marriage additions, and the rest. But now in some states they are compelled to take them all. Their banners, logos, signs, and name are being associated with something contrary to their religious standards. This is not right.
The way around this is to set a generic, non-discrimatory policy that they will perform marriages only for members of their own congregation. Everything else is just a money-grab. If a minister is out there in the world at large, offering to sell his or her services as a marriage officiant, then that minister has forfeited all right to pick and choose who they will marry. Similarly, if I were of a persuasion that is discriminated against, do you think I would WANT a photographer or caterer or florist who disapproved of me or my lifestyle? No way! I wouldn't try to hire that person in the first place, because they're not going to put their best effort into the product, whatever it is.