separation of church and state

Are Church & state separated? Because if they absolutely were, they would allow gay marriage? Instead of Civil Unions which do not permit the same legal rights as "a marriage" does. This leads me to believe that the church still has influence over the government.

I asked my mother why shouldn't gay people be allowed to get married? She responded with this, "A marriage is between a man and a woman, not a man and another." But if America is a place where "All Men Are Equal," shouldn't everyone have the same rights? She said that there are Civil Unions for that. But they're not the same I thought to myself. As David Watters has already posted here discussing Civil Unions versus marriage.

How does the church have power over or through the government? Many (moral) laws came from the bible. And not all should be disregarded, since it did tell the government that men should not murder another.The bible didn’t say that homosexuals could not get married. But religious leaders today do. But why?

I'm a libertarian and I believe in rights to and for the people. And government officials should take the constitution seriously when it was written "All men are created equal..."