King Daniel wrote:
Admiral Marcus calls John Harrison "one of our top agents" in the last trailer, which screams Starfleet Intelligence to me, not the rogue group Section 31. They wouldn't answer to Starfleet or their commander.
Section 31 seemed to remain an extremely covert organisation in the Prime Universe for centuries. Perhaps they've become a bit more widely known about, having been exposed sometime after Nero arrived. Bound to be some knock-on consequences which have altered that version of the 23rd Century, which can explain Starfleet openly working with their own little CIA.