As tempted as I am to dismiss the Section 31 speculations, knowing how well steeped Orci and some of the others are in Trek esoterica does make me wonder. We also know from some of their comments that a certain degree of relevance to current events was desirable in this film. I could imagine a scenario in which John Harrison is actually a Section 31 operative, perhaps genetically augmented, who was somehow betrayed or abandoned by his superiors. Peter Weller might well be the head of Section 31, operating from a secretly built, technologically advanced starship, maybe the one with the darker interior we've seen in the previews, and maybe even the one we see crashing into San Francisco bay. All kinds of potential there for commentary on shadow governments, corruption, compromising of principles, abandoned loyalties, etc, and none of it requires an established character like Khan or Mitchell or even Unnamed Redshirt #7.
You know, I wonder if the statements that were made about the "villain" being a character from TOS season 1 were not in reference to the Cumberbatch character but rather to the Peter Weller character. Maybe he is one of the admirals who occasionally appeared on-screen to deliver orders to Kirk and the Enterprise or someone similar. The statements would then technically still be correct.