I don't give the transporter scene in NuTrek a pass because it lacked all subtlety. A brief (and I mean brief) TOS style finger touch which catches Kirk's attention would have preserved their professionality, have as much significance to the couple (Vulcans are telepathic), and could have been underscored when Spock tries to give her a final message later. They delayed quite a few precious seconds snogging and emoting when an entire planet was at stake. It was dreadful.
The entire point of the Spock/Uhura transporter scene was to show that Spock was out of the closet. No longer hiding the fact that he has emotions, no longer hiding his affection for Uhura from the world.
You're so caught up on military protocol (how often has Trek cared about such things?) that you've missed the point of Spock's story arc, his coming out alegory. Which is sad. Everyone sees, they're all a little suprised, but they all accept it without question.