Protect Marriage Amendment and Churches Rights

There are protect marriage amendments up for vote in at least two states that I'm aware of, California and Arizona. Opponents of these efforts often criticize the LDS church for supporting these measures. Unfortunately, in today's political and moral climate, standing up for one's beliefs is often mistaken for intolerance by those who do not share that belief. This post is not about whether or not the protect marriage amendments should pass, but rather addresses why a church (like the Mormon church) has a right to be involved in the process. The protect marriage amendments are not fundamentally about discriminating against people who are gay. Their primary purpose is to seek to recognize the institution of marriage as between one man and one woman in law such that a judiciary cannot arbitrarily redefine what marriage is. The amendments as they currently stand do not seek to restrict any of the civil rights already granted to gay couples (things such as hospital visitation rights and others). So why then even need a marriage amendment? Why not let gay individuals marry just as a man and a women can?