It is a bit different, because with respect to schools, it was easily shown that the "equal" part was not true. The schools were not equal in any way, shape or form. With respect to handing out marriage licenses, it could be equal. The recipient has no vested interest in whether her license is signed by, and handed over by Mary, or by Fred. The license is the license. So "separate but equal" is not the problem here. The problems lie in the fact that the County cannot, and should not, set up a system that creates inherent humiliation due to sexual preference. A same sex couple should not suffer indignity at the hands of the state by having certain state workers turn their backs on them and refuse to help them. For Mary to say: "I refuse to help you. But Fred here will take good care of you" may seem like a solution for Mary. And Mary might think this is a good solution for the couple who wants the license. But it does not remove the feeling of humiliation that can ensue by having someone tell them that they are not good enough or worthy of the paid employee doing what she is supposed to do according to the law. In essence, she is saying, "I refuse to follow the law, but that's OK, because others will in my stead.
The other problem comes from the fact that a County could run into a situation where all of the clerks want to "conscientiously object". If the State allows for "opting out", and everyone opts out, what then?