Marriage and Holy Matrimony are not the same thing and never have been. The fact that they are often performed together is at least partly responsible for the misconception that they are one and the same thing.
In marriage, the state joins together. In Holy Matrimony, God joins together. When a clergyperson officiates at a church wedding, he or she is also functioning as an agent of the state. That may now no longer be the case. We have to wait and see how religious liberty is considered in the future.
I have long wondered if the gay community would have been satisfied with a civil union law that would afford all the same civil rights as heterosexual couples enjoy, but not call it marriage, the issue would have been less contentious.
I am aware that some churches that identify themselves as Christian perform gay marriages, but the majority do not and are not likely to do so. Whether they will be able to refuse to perform gay weddings under this ruling is an issue that the dissenting justices made note of. Things like tax exempt status are issues that will surely surface in the future as we learn to live with this new reality. For the majority of those that identify themselves as Christian, Holy Matrimony will always be understood to be the life long union, ordained by God, of one man and one women.