I was surprised not so much at the mention of Section 31, but at the admiral talking about it quite as openly as he did. Perhaps he didn't think it was a problem because he didn't intend Kirk and Spock to come back from their mission, but still, if Section 31 is supposed to be the ultra-secretest of secret organizations, you don't just blurt out that they exist where anyone can overhear you. It makes me think the writers tossed it in so we'd be happy with a DS9 reference without really understanding what it is that makes Section 31 what it is.
BTW, are we supposed to assume that the admiral was actually a member of Section 31 himself? He mostly came off as your average Insane Admiral TM, but actively trying to start a war because you believe it's inevitable but you've got genetically engineered supermen on your side so you'll win anyway does kind of sound like a S31 thing. And the secret base and secret starship with its non-official Starfleet uniforms also fits.
I was surprised by this to, that the Admiral was so forthcoming about the existence of Section 31. Though when you think about it, even DS9 and Enterprise sort of established that Section 31 hides in plan sight. That being said, on DS9 you got the impression that even the mention of Section 31 was a risky act.
Someone in one of the Into Darkness threads suggested that the destruction of Vulcan had scared or hardened Starfleet/Federation enough to bring Section 31 more into the light and I can accept that. I mean they could argue that the destruction of Vulcan proved that they were right and were necessary to deal with other threats. (Though personally I think the film undercuts this by making the adversaries the admiral is gravely concerned over very weak).
I had a feeling Section 31 would be in the movie after reading the Countdown to Darkness prequel. The story there gave me that kind of feeling and the aftermath made me real suspicious. As for the film itself, the admiral's plan did sort of fit in line with some of the crazy plans we've seen on DS9 and ENT. And I also got a vibe from the Section 31/DS9 novel "Abyss" with Harrison.