I would have been so much happier with the film if John Harrison had just been a kick-ass S31 operative with access to loads of classified technology, rather than what they turned him into (I actually groaned in displeasure in the cinema when the reveal was made).
Totally agree. As soon as Section 31 was mentioned (by that racist terrorist guy from ENT, weirdly enough!) I was so jazzed. "Fantastic!" I thought, "Abrams has made a Section 31 movie! At last!" That positivity and optimism carried right on upto the moment when John Harrison did his big identity reveal (after having the Enterprise's hairdresser sort him out in the ship's brig) and all my hopes for a genuinely creative and thought-provoking movie crumbled faster than Abrams' Vulcan.
For the record, I would argue that the existence of Section 31 is part of what makes (proper) Trek great - the shades of grey. Odo summed it up better than I could - in a universe where the Tal Shiar and the Obsidian Order exist, it is illogical to assume that the UFP wouldn't have something equally shady and nefarious.