I hope it's Section 31. I love Section 31 (kind wish they'd get their own Spin-off show/Film).
Also, something just occurred to me. Could Alice Eve be working with Benedict. In the scene where He is beating the living crap out of Chris, it looks like she's really conflicted.
Maybe Admiral Marcus is actually working with Harrison and has got Carol onto the enterprise to spy on Kirk and the crew going after Harrison (and if Section 31 is involved than all 3 of them could be in it with Marcus being it's head).