Marriage is a religious institution which is honored by the state. Because we, as a nation, are intended to separate the concepts of church and state, it only stands to reason that marriage is purely religious, and that civil unions or domestic partnerships are the accepted and acknowledged legal bonds which should be honored.
Still, it'll allow the church to protect their "sanctity of marriage." As viewed by their respective deities.
The married couple will still have to file for a civil union/ domestic partnership just like everyone else they wished to exclude from their marriage in order for the government to acknowledge such a union. Only then can those partnerships visit their loved ones in the hospital or file inheritance claims. etc. It may not be desired, but it'll be fair.