Section 31 in the film isn't quite the same as it was in DS9 - it seemed to be more of a militia than a black ops organization.
They seemed more like a special research branch tasked with developing experimental prototypes, long range stealth torpedoes and portable Transwarp Transporter devices to name 2.
If I had to have an explanation for the change, what ever the reason be it the destruction of the Kelvin or Vulcan, S31 became more 'public' at least within Starfleet in a way that the secretive SAS became public knowledge. The public face is probably just the beginning with the R&D.
Hide in plain site and all, better to have a cover for some of their goings on plus some of what they come up with can be fielded to improve the general fleet.