I was under the impression they were already involved at the beginning of the movie, that Uhura bringing Scotty "dinner" on the bridge was an indication they were in a relationship. Or at the very least, more than friends.
Yeah, and it's implied that they had plans to spend Shore Leave together, but he got caught up in his work instead . . . . But I'm still want to blame it all on touch-feely emo mind-melds and make it all Sybok's fault. At least that's my story and I'm sticking to it . . . .
Scotty/Uhura were under a spell. Lets also remember they were a couple in a terrible film. So of course the relationship is terrible as well. I like a Trek couple when the romance is well written this is another reason why I have always hated slash fan fictions. Its so OOC and unnecessary.
Uhura and Chekov went on shore leave together in the original series too. He was even affectionately teasing her because she wanted to go shopping all the time and he had to go with her. If they were all friends when they were young it's only natural for me to imagine that they were all the more a family when they got old so in that I don't see flirting between Uhura and Scotty or a hint that they were a couple. I almost see her acting like a mother tbh. In fact, in a magazine Nichelle Nichols commented it saying that they were just friends and their interactions were influenced by the friendship between her and James. Anyway, in the other scene later she definitely WAS under the influence of Sybok. It's even stated in the script. I don't think we could infer they were already dating before that because otherwise the dialog in that scene wouldn't make any sense, Sybok's influence or not, since Uhura said that Sybok had put her in touch with feelings she has never expressed before. Had them been a couple you'd get an explicit hint of it in the end or the next movie that we never got. If anything, even in the DC comics sequel they say that she wasn't herself and they remain just friends (you can read the scan here: http://www.chud.com/community/t/115578/the-star-trek-thread/2050#post_3021156)
The whole Spock/Uhura in the new movies is something I do not like, but it does give us something new to watch besides examining how closely the new actors imitate the classic roles. I mean when you see Chris Pine do the little 'Kirk-Hop' when he goes over to his command chair at the end of the first move I smiled- he got that little nuance down right, but I did spend most of my time watching the actors try to match the performances of the original cast, being those people we were sop familiar with. Having the S/U relationship pop in from left field was weird, but it did reconfirm that in this rebooted universe all bets were off...
Scotty's reply about "Lassie...you're the most understanding woman I know" would also seem to bear this out.