Yep, it wasn't until those pictures of him and Spock were released did they admit he was the Villain.Whom? That was reported from the get go and even Cumberbatch himself has said that he is portraying the villain.
At the very beginning I think there was a quote from JJ saying he wasn't necessarily the villain, and Cumberbatch in an interview said he might or might not be the villain. But everyone really knew and since then, you are right, he's been straightforward in interviews that he is playing the "not-so-good-guy".
Pegg also said back in December that he heard no mention of the name Khan in the script. Yet the confirmation from AICN and Trek Movie say otherwise.
I am not questioning that Pegg isn't a stand up guy. I just get the impression he is trying to keep things fun and mysterious. He's the only cast member to deny Khan is in it.
Well, aren't the "confirmations" by AICN and Trekmovie just confirmation of rumors? Even if they were from high sources or multiple sources, they're still just rumors. I dont think any official source has said anything on record and by name, yet.
As far as fighting Spock or being shot by Uhura goes, that means he must obviously be doing some kind of "no-no," but it could be he was an otherwise fine fellow in the movie until then, then he became under the influence of something that turned him.
Maybe I'm spinning things to my expectations, but I'm hoping that the ambivalence around whether or not Cumberbatch's character is a "villain" centers around being a bit more complicated than that.
The longer we wait, the more we'll say, "WTF" if it's finally revealed he's not Khan, or, "Why didn't you just say so in the first place?" if it is.
The timing on being coy about something and getting the desired result from it is tricky. Leading people on a merry ruse is one thing. Playing them is another. At some point, the publicity payoff will be anti-climactic if it is really Khan.