If the people of the U.S. decide that same-sex marriage should not be legal, then that is what the government should support, regardless of the rationale behind the sentament. Likwise, if the people decide that same-sex marriage should be legal, then again that is the choice of the government, regardless of the church.
But long time ago, the people of the US decided that all are created equal, and that discrimination should not be tolerated. That trumps all else. Or should we still allow slavery, and deny women the right to vote?