Many fans thought that the true identity of the villain known as John Harrison has finally been revealed to be Khan when EW printed a pic of Cumberbatch alongside Star Trek Into Darkness co-star Chris Pine, with the headline "Kirk and Khan". Although just as many believed (apparently rightfully so) that thsi was merely a misprint, and not the leaking of some big secret by the mag at all. In the below vid Alice Eve is asked about it, and flatly states that he is NOT playing the classic Trek villain.
Of course this still doesn't really prove anything, as we all know that stars and directors will flat out lie about such things to keep secrets, but in this case I think we're going to have to resign ourselves to the fact that we will not be getting a new take on Khan Noonien Singh in this
Star Trek sequel.