Now that same-sex marriage is the law of the land in the United States and in many other countries, plenty of people are asking the question: should clergy that refuse to perform same-sex marriages be protected? This question is complicated by the fact that no one asking this question is going to have an unbiased view. The people who try to have an unbiased view and who are arguing in favor of individual rights and religious freedom are going to be supporting the conservatives in practice, even if they do not support them in principle, which is going to polarize the issue even more.
The people who argue that there should be protections in place for the clergy in question are arguing from the standpoint of religious freedom. However, religious freedom is not going to get people off the hook for everything. The people who commit crimes and who say that they did so because their religion warrants such crimes frequently do not receive religious protection, even if that is the angle that their lawyers will try during the trial. The clergy members who do not perform same-sex marriages are going against what the law of the land says and failing to recognize the manner in which laws have changed, which seems to indicate that they have strayed into territory where religious freedom offers no protection.
There is also the fact that plenty of religious people do support gay rights, even if their churches technically do not. Plenty of individual clergy members are fine with same-sex marriage, and they will perform same-sex ceremonies. These people clearly do not believe that their religions are incompatible with the tolerance of gay people, so it seems that the clergy members who do are using their religion as an excuse for their bigotry in practice. It is also important to note that there are plenty of gay religious people as well, which will complicate the situation further.
People often regard religions as being the sorts of institutions that never change. However, this is empirically false. The Church of England once scoffed at the idea of female vicars, and they are now common. Gay vicars were once controversial as well, but this stigma has started to fade away in recent years. The stigma against same-sex marriage in most religions is not the sort of thing that is going to last forever. Society is tolerating LGBT people more, and churches are going to need to change if they have any intention of staying relevant. This trajectory is inevitable, and even many conservatives have given up on trying to hold onto their homophobia. In a generation, many churches are probably going to sweep their history of homophobia under the rug.
However, if clergy are protected from their duty to recognize same-sex marriage, this natural process is going to be circumvented. The churches are going to be frozen in time, and they will not adapt according to the right process. Society should not allow this to happen.