Marriage license rejected on lack of religious affiliation?

Yesterday's Pittsburgh Post-Gazette featured a story about a couple trying to obtain a marriage license that does not require an officiant. According to the article:

According to the lawsuit, the couple applied for the self-uniting license on Aug. 29. But they were told they would have to supply documentation that they were Quakers or members of the Baha'i faith, who believe that there is one God and that all humanity is one family.

Otherwise, a supervisor told them, the register had been directed to stop issuing self-uniting licenses.

I don't think the state and/or county should be able to decide or receives a certain type of marriage license based on religious beliefs. Isn't that what separation of state and religion is all about? Also, shouldn't the standards be the same across the state? Butler County doesn't even offer the self-uniting option. A license issued in any county can be used for a wedding anywhere in Pennsylvania, so the rules should be the same across the board.

What do you think?