That is incorrect. SCOTUS cannot change the plain language of a law (Obamacare notwithstanding).
SCOTUS held that it is unconstitutional for state law to not allow for homosexual "marriage". KY law explicitly disallows homosexual "marriage". SCOTUS, therefore, invalidated KY law.
The KY legislature has not replaced that law. Therefore, there is no operable law for the creation of marriage licenses.
The homosexual "marriage" decision by SCOTUS is, legally, even worse that Roe-v-Wade. In Roe, SCOTUS invalidated laws banning abortion. Roe did not require states to do anything, but rather not to do something. In the homosexual "marriage" decision, SCOTUS invalidated laws, but also requires states to affirmatively recognize and perform homosexual "marriages" regardless of the actual statutory authority to do so.
Finally, if the clerk has to check her religious beliefs at the door (to borrow your phrase) for this elected office, despite the absence of actual law requiring homosexual "marriage", how can this not be considered a religious test for office, which is expressly forbidden by the constitution?
I will bet there is no Kentucky law that orders county clerks to issue marriage licenses. They do so by custom in Kentucky and all over America. They also do it to bring in some money.
IOW it is traditional, logical and common sense for Kentucky county clerks to issue marriage licenses but there is no Kentucky (or Federal) law demanding they do so.
So I don’t see where Judge Bunning gets off demanding anything from clerk Kim Davis