I have less of an issue with her behaviour here than I do with the way she was portrayed in the Transporter Room.
Whatever they do with the relationship in the next movie I really hope they leave it in the bedroom. The more it interferes with their decision-making while on duty the more we have to wonder why one of them isn't transferred!
It is obvious to me, that someone high up knew about their relationship, which is why Spock didn't want the "appearance" of favoritism. . .but she is obviously a graduate student (given her rank and the fact that she was once the TA in his department. . . even in today's society, professors and grad students are allowed to get together) so, it's not necessarily against the rules. . . for instance, George and Winona Kirk serve on the same ship, and he's the First Officer. . . you look at Star Fleet in the same way you look at today's military. . . they are not going to send a bunch of young people out in deep space for years at a time and expect them NOT to hook up with someone. . . btw, Spock
pulled Nyota onto the transporter pad for the kiss. . .as he stated, his odds of coming back were less than 5% and his father has just given him permission to be as emotional as he needs to be. . . I think a little leeway is allowed in circumstances like that. . .