They say that according to the North Carolina Constitution they suffered discrimination. Did you read the North Carolina Constitution’s relevant sections?
Yes. The relevant sections are, in essence, the equivalent of the First and Fourteenth Amendments to the Federal Constitution, and say that all persons have the right to right to worship as they choose, and be free of discrimination based on their religion.
The point is, there is a distinction between how one acts as a private citizen, and how one acts as a representative of the state. The state itself has no religious beliefs. So, a magistrate who is acting in his/her official capacity, is acting as an agent of the state—that is, without religious beliefs—not in their individual role (with their individual religious beliefs). Saying that the magistrate may not act based on their own religious beliefs while acting in their official capacity does not infringe on the magistrate’s religious freedoms.