You're right, you are smarter than arguably one of the best political philosophers of our time. How could I have been so dumb to assume that you weren't smarter than him. If you had ever read Mill you would understand what I am trying to argue.
He would argue that because (in California) because a decision was passed in a free election, the decision stands. Furthermore, he would argue that there is a legitimate reason for passing this law because certain groups cite moral problems with gay marriage. He argues that laws preventing harm to morals and all other things besides that cause harm that is not physical are legitimate.
That's my point. It's not an argument, for the most part, about religion or homophobia. The argument is that gay marriage would cause some harm to some people. And that is what the Californians decided.
I was simply using the creation vs. evolution argument to cite an example. But you already knew that since you're smarter than Mill.