For the non nerds Section 31 is a organzation that works indepently from the Federation to maintain the stability of the federation. Bascially space cold war shit. It was created to counter balance the Utopianess of the Federation. You know, everyone loves hot dogs, but no one wants to know how they are made. It feels this runs against Gene's original idea for the series. The Federation has never been project as perfect enough that this level of cynism needs to be injected into it. In the novels they already been taken down by Picard, Bashar, and short Dax.