There Are Two Marriages
The key point that's being made, as I see it, is that the concepts of marriage and civil union, long considered synonymous, should be broken apart into their component elements. The state has an interest in civil union, for purposes of tax law, inheritance, etc. The church hasn't (or, rather shouldn't have) any interest in those matters. Marriage, on the other hand, is a sacred union, binding the couple in the eyes of the church, God, and each other. The state has no interest in that aspect of the relationship.
Looked at from that perspective, I can't see why the state would have any concern about the gender of the parties involved. If the church feels that a given union is not right in the eyes of God, then by all means they should not sanctify it with marriage. I disagree with that stance, but I respect that their views are held with honest conviction.
Be that as it may, that's completely separate from the interest of the state, at least in this country.