The problem is that "marriage" has two meanings, a legal one and a religious one. So technically, state-sanctioned "marriage" is at least potentially mixing church and state. (That is, in fact, precisely where this whole issue comes from.) By defining a legal "civil union" which carries the legal aspects of "marriage" without implying the religious aspects, you remove the anti-SSM argument as well as potential other arguments (consider how interracial marriage used to be regarded).

This also makes it crystal clear where the "defense of marriage" argument comes from: it is nothing more and nothing less than ensuring that an essentially religious concept is enshrined in law.