As I've mentioned earlier, there are even some cases where two people are viewed as religiously/privately married, by their church or family, but don't consider themselves to actually be married, and are not married civilly.
The bottom line is that civil marriage should be completely secular. Religious beliefs should have no say in who can be involved in a civil marriage. Now, the government can limit civil marriages, but those limitations should be fair. The best thing the government could do is to explain exactly why it endorses civil marriages, and make the civil marriage laws fit with that reasoning. As the marriage laws are right now, they discriminate against homosexual couples without a good reason why.