Kentucky law defines marriage as a union between a man and a woman. The Supreme Court ruling is just a ruling, not law. All law is enacted by congress and signed by the president. By not issuing marriage licenses to same sex couples, she is upholding the law. By not issuing them to straight couples she gets into trouble.
Rulings are not laws, but they will continue to be given the weight of laws until Congress stands up for their rights and responsibilities. Much as the company will continue to ignore the contract until the members force them to adhere to it.