Churches have the right, as does any private institution to dictate who among them has what privileges while a member of that institution (so long as they are legal). In this case, that right would be marriage. If churches (read synagogues, mosques, etc...) do not want to marry homosexual couples then they are free to act upon that belief.
But when we as Christians, Muslims, Hindus or any other faith member begin to endorse laws that promote separation and segregation, we are always wrong.
I have long believed that not every person of faith belongs in politics, not because they would be more apt to insert their beliefs into law (our laws should be based off of the most uplifting moral code that we as a faith community can proclaim), but because not every believer fully understands that in America, your beliefs cannot and must not encroach upon mine in any way that dehumanizes or degrades my choice of lifestyle, sexual orientation, race, religion, or economic status.
In fact this issue is a wonderful opportunity for people of faith (of which I am one) to demonstrate the unconditional love of God and welcome into the fold those who have been abandoned to the fringes of society and deemed second-class citizens. Much like slavery and the institutionalized segregation of blacks in this country, our treatment of homosexuals will be yet another time in our Christian history that we will ultimately regret. That day will come when we stop believing that God is always on our side, and hope and pray that we are on His.
This One Generation is the voice of change and hope that is needed in the world with the courage and will to bring that vision to life.