I agree civil unions would seem to address this though you have fair and equal under the law, do you need a marriage in a church to have a partnership with equal rights under the law?
Most Christians including CivGeneral would not be opposed to a right of partnership outside of marriage, essentially it's the same thing though with equal conditions but no affirmation by the church, I'm sure most people could agree to that. I think the church has every right to deny it's traditions on what it believes as marriage as a religous union, and the government has every right to accept unions outside of those beliefs, I see nothing wrong with that. And I see no conflict other than a semantic one, marriage/civil union same deal.