Personally, I doubt J.J. & Co. would mine that far into the lore. That's not an indictment of their writing abilities or their Trek fandom, mind you; it's just that Section 31 is, relatively speaking of course, some pretty obscure stuff. It feels much more likely to me that they'll rework more classic or commonly known elements - Romulans have been done, Klingons are the logical progression, Khan - before getting into any of the "deep cuts", most of which would probably be left for comics or the possible new TV series.
That said, I'd rather see a Trek film with such an ominous subtitle as "Into Darkness" deal with heavier subject matter. That's not to say that a Klingon or Khan story done properly couldn't accomplish that, but Section 31 would be right up there with them. As would anything Cardassian, but again, that might be drifting too far away from the core Big Bads.
But hey, if we're shooting about the heavy stuff, obscurity being no obstacle, and presumably we've got a human antagonist this time... Colonel Green? Terra Prime?