As I have said before, the solution is to have same sex licenses issued by the state. In the courthouse have a dot matrix printer hooked up to a state web site that generates the very special same sex licenses. Put this PC/printer in the corner of the marriage license office and it is self service and requires no personal contact from the local county officials.
Why don’t we just go one step further, dump all these clerks and paper-bureaucrats....and have everything done via a web-site at state level and you print it out at home. Charge the requirement off your credit card, and if you want some marriage ceremony conducted....pay $60 extra and a Skype session will start with some on-line minister or state-approved minister.
I don’t see any reason to have clerks around except for car registration purposes. My hunting license was granted via a on-line registration last year. You should be able to dump half the clerks in any state office operation by going to this route.