The solution is to get the church out of the government marriage business. Churches perform Holy Matrimony, a ritual of the faith. This need have nothing to do with state licensure.
Holy Matrimony is a joining of a man and a woman in a marriage blessed by God and faithful to the body of Christ. The preponderance of couples living together without licenses from the state demonstrates the bankruptcy of that system. These same couple make serious commitments to each other that the church has the unique ability to bring into the body of faith, thereby sanctifying that marriage.
Unless the church wants to marry Bob and Brad they had best sever all ties with the government marriage licensing system.
In essence, SCOTUS affirmed that marriage (which IS Holy Matrimony) must now be afforded to same sex couples.
Churches will be forced to perform same sex ceremonies, or they will be punished.
Mark my words.