The "best" solution is to keep the legal rights and priviledges as a contract with the state. That is to say, that the legal part is simply legal. And the religious part is simply religious.
Everyone has to get a "civil union" (straight or gay or whatev) through a legal contract, but whoever wants can have a "marriage ceremony" with whichever church/religious organ that allows it.
If I'm able to articulate what I mean correctly that is..