with the caveat that all i know about this is what i've garnered reading this thread, it seems to me that the clerk should be fired, but not fined or jailed. if there are civil or criminal charges for denying the couple their civil rights, they should be imposed on the clerk's employer, not on the clerk.
my rationale is principally (but prolly not fully), based on the idea that since the clerk hasn't even been fired, the clerk's employer likely did not fully explain to employees the job requirements and penalties for failing to fulfill their duties. if the employer can prove that it did explicitly inform employees that they have a duty to serve all citizens and what consequences for failing to do so would be, and the employee chose to disregard those instructions, then perhaps the employee should have some personal liability beyond dismissal.
all of the above is based on ethics, not law. i have no idea what the law says.