It shouldn't. I've been vocal in my support of eliminating marriage as a legal concept and replacing it with civil unions for all. But until then, there's no reason to enforce existing law unequally.
Again, marriage is available to all. The law treats no one unequally. And I agree with you 100% on the matter of state-recognized civil unions, and the state not recognizing religious marriages.
And yes, saying that only marriages meeting the religious definition are valid is applying the law unequally. It's like passing a law banning pork, and then saying that it's fair because it applies to everyone, whether their faith forbids pork or not.
Different matter entirely. Laws banning smoking? Or Alcohol? Or Big Gulps? They have nothing to do with the Equal Protection clause.