Kim Davis and the KY Clerks Association tried to solve this before it became an issue. They petitioned the in-session KY legislature to remove the clerk’s signature from the certificate.
The evidence doesn’t support your suspicion.
What goes on publicly need not be same as what goes on privately, especially with politicians or homosexual activists.
E.g. she also petitioned judge with similar request, but both could have been part of the same game choreographed for the public consumption. If she is playing her part with judge, she could have been playing it with other collaborators in the legislature. The house there has Democrat majority if I recall correctly anyway (not that "Republican" label means all that much more than the money that bought their office last).
Frankly, I don't trust any theater politicians, bureaucrats and the cronies buying them are playing for the public consumption. My default assumption is that the scum that floated to the top of their cesspool is lying to us as usually.