Churches and other religious institutions have always been able to discriminate in their hiring, in who they marry to each other, and so much more. They can discriminate against all sorts of protected classes and that did not change in June. Again, same-sex couples are not in a class of their own where everyone is required to accommodate them all the time- no one is. The Supreme Court has ruled many times, including very recently, that religious institutions can discriminate against protected classes. Conservative churches do not have to hire female pastors. Catholic churches do not have to perform marriages of previously-divorced people. I do not see any evidence that this is breaking new ground.
I just don't think this is anywhere near as big a deal as some are making it out to be.