Licenses to marry are like being forced to get a license for a dog. They make no sense.
Well marriage doesn't make sense either. Why do people feel the need to marry? Often people see it as security, false security. Seeing as 40% of first marriages end in divorce, a marriage doesn't offer anything. Doesn't stop cheating, doesn't stop problems, often causes problems.
I've been in relationships where the person suddenly gets complacent and then it goes downhill from there.
I've known someone whose parents never got married and they're still together 30 years later.
Marriage doesn't do anything except for give legal guarantees, like with inheritance and tax breaks and so on.
There was a gay couple, one guy adopted the other one so they could get most of this legal stuff. Then they had to unadopt so they could get married now that gay marriage is legal. It wasn't the marriage that was important, it was the being together.
The license is merely a way of giving many people what they seek from marriage. The feeling of security, the ritual, the telling everyone how much they love each other, the looking like a princess, the same surname (in various Western cultures) and so on.
It is legal agreement and licenses are issued by the state. A person's religion has nothing to do with it.
The clerk should have followed the law. She is not being asked to perform the marriage ceremony in her church.
Her job required her to issue the license without prejudice under the law of the US.
Now she will spend an undetermined time in jail, and possibly her son will soon be there as well.