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.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.
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.
I think JJ made a mistake thinking that finger-touching would not be understood. We saw it for the first time in TOS and we understood it. Did people get dumber in the last 40 years? It's all in the presentation i.e. it could have been established in an earlier scene in addition to kissing.
For me it isn't about military protocol though. I feel exactly the same about similar scenes in the movie '2012' when people are wasting time hugging while a woman is drowning in the next room or while the ship needs emergency repairs or everyone dies. When seconds count and lives are at stake I find sentimental indulgence to be offensive.

Plus, I didn't fail to understand Spock's arc at all - compromised as his emotions are, I might even overlook his conduct but Uhura has had emotions all along. It belittles her as an officer to show HER emotions take precedence at a time of such crisis. Why is it always about the man?

And again, Kirk and Spock go it alone in order to cement their friendship when in fact sending a fluent-Romulan-speaking technician, a med-tech (for Pike) and a couple of security guards would have made far more sense.
If the scene had been briefer, I would probably have let it pass but it drags on and on to the point where they are obviously wasting valuable time. I'm all for Uhura and Bones getting more time but not if they're just tools to make us love Kirk and Spock all the more. Let them be their own characters.