Here's what I don't understand about the gay marriage debate:
1. Are there any salient legal differences between heterosexual civil marriage and a homosexual civil union other than the name? Can two people in a civil union file their federal income tax as married?
2. In this modern day, why is the government even involved in (heterosexual) marriage in the first place? Wouldn't it be possible to split marriage into:
A) The religious part, called "marriage", which is handled by your church (or not) as you please.
B) The civil part, called something else to soothe tensions. Maybe it could be called "standard contract between two people granting hospital visitation rights, inheritance and standard government tax breaks".
If this happened, then part of the gay marriage debate (A) would be moved into the churches where it belongs (for example, LDS would be free to ban gay marriage among Mormons if they wanted to).
The other part of the gay marriage debate (B) about equal protection under the law would be about something that was no longer called "marriage" and wouldn't inflame so many emotions.

nope we're screwed
The federal govt. doesn't recognise civil unions or gay marriages that are legal in states like MA. So no, we can't file as married. If the state you're in doesn't recognize your union then you won't be able to visit your partner in the hospital, and if anything happens to your partner and the kids were legally theirs you may loose them to other relatives or the state because you have no legal say in their wellbeing.
But you're right. The gov't should have no say in the matter. Marriage is a religious institution, and as such should be up to whatever church you happen to attend. However, I do recognize that if the Govt. stops mucking about with the religious aspect of it we do need some legal concept to recognize that 2 (or more (again i see no reason the govt. should get to decide the number of people allowed to be legally joined, since in many religions multiple partners is acceptable)) people represent a grouping with atypical connections. Legal couples should be responsible for each others bills, and be able to visit the other in the hospital, and be responsible for the children regardless of who's genes they hold, and all the other benefits and complications that married straight couples get.