A few things:
Hillary isn't subject to the UCMJ. The sailor is. There are several articles of the UCMJ that he can be prosecuted with that Hillary can't. The big ones are Article 92 (Dereliction of duty, failure to obey a lawful order) and Article 134 (Conduct detrimental to good order and discipline). These were the same articles that they nailed Chelsea Manning with. The UCMJ couldn't care less whether the contents of the sub were classified or not; all they have to focus on is that the command said, "Do not take pictures of this shit," and he did it anyway. That's a crime in the military, even if "this shit" wasn't even classified. The fact that it's classified material just increases the magnitude of the punishment.
The civilian law that covers Clinton requires knowledge that the material was classified. The FBI said that they didn't think that she knew it was classified (which is bullshit, but we're going off of their thoughts). In contrast, the sailor knew completely well that his job was classified - there's a reason why annual training and constant 4-hour briefs get hammered into you.