two simple solutions I've been advocating for awhile.
All "charitable" organizations can recive tax status based on how much actually gets based on to those that need it (recruiting and religious education would not count toward this). So if a church runs a soup kitichen and 50% of its money goes there it gets a 50% tax break, and those making donations can deduct 50% of the donation. In the case of the WTBS, none of the money goes anywhere so the tax break would be zero.
I don't think the government should be marrying anybody. States could set up some sort of domestic partnership (a modified LLC) for those that want it. If you want to be married you can get a church or somebody to do that, but it would be a purely religious function.