io9 addressed the tweets on Monday in a tongue and cheek manner, saying "Good. If we're going to start blasting IMAX shots of naked medical/science officers for no reason besides, because they could, at least give us a few Bones pics." But was sure to add they thought the scene was ridiculous. My feelings wouldn't be hurt if the scene wasn't in the movie, but I often notice there isn't much of an uproar when the situation is reversed. My biggest issue about it was that it was used in a viral video campaign for the movie, putting the scene in a spotlight that made it stand out. If you are going to point to the men being half naked as well, yet not highlight them, you can't be surprised the scene would get extra attention from fans.
What I found more interesting was a blog post from actress Felicia Day about the movie where she took notice that the movie was lacking in strong women. Feeling Carol Marcus (pictured above) served as little more than damsel in distress and Uhura mostly only served to humanize Spock. Mainly she points to the scene where Kirk and all the Admirals are sitting around the big table and get attacked, not seeing any women there. I think she is on the money with that specific point and think they could have been well served by having a woman or two sitting around the table (unless there was and both her and I don't remember).
That being said, I do think the female leads have some good qualities as well.
(Beware Spoilers) Carol Marcus is not a warrior, she his much more like Scotty who isn't going to fight his way out of every situation with his fists. She saves the Enterprise by confronting her father and then is put in a situation where, yes, she does need to be saved, but so would any of the male characters put in that situation (ala Pike in the first movie and Scotty who they are rescuing along with Carol). But nobody notices when a dude in distress gets saved, understandable I suppose, but at least take notice when the situation is flipped and it's the woman rescuing the man. Carol Marcus also saves Bones earlier in the movie by risking her life, and just because she doesn't do it with a spinning back kick doesn't mean we should overlook it.
As for Uhura, I thought that her confronting the Klingons alone was a pretty big deal and when the shit hit the fan, she was right in the mix with everyone else in the fight. Not to mention she played a key role against the villain in the climax. I don't think either of these women were treated badly in the movie, a franchise that is pretty much about the three-way between Spock, Kirk and Bones, where everyone else is a second tier character next to the trio. Some characters orbit a bit closer than others to the trio, Scotty being one of them, and in the new version of Star Trek, Uhura is now there as well (and not just because of her relationship with Spock).
There is still a long way to go befeore institutionalized sexism is pried out of entertainment, but Star Trek is, at least, trying to make some progress and it's nice to see Lindelof take notice of what they still need to work on. Hopefully he'll take notice of not just the main cast, but how the world is fleshed out with extras as well. Star Trek once set the bar for being ahead of the curve on issues like this, so it's something that fans will be watching out for.
Mostly, I think this is about sensitivity to an issue close to someone's heart. Nothing wrong with that, but once it is brought to the masses on the internet it grows from there, and it can overshadow the good points about the film.
The film isn't perfect, but it's not a disaster either. If there is a number one complaint about Star Trek Into Darkness, it should be about how Cumberbatch over-enunciated everything.