The weird thing about Section 31 is, if all the novels are to be taken as part of one's personal canon, that means that for a secret organization, they've been pret-ty damn loud. The Enterprise Incident and TUC come to mind. My only complaint about Section 31 is that a lot of negative things that the Federation or Starfleet has EVER done on screen is now retroactively accredited to the group, which suggests a very haphazard leadership.
Heck, if we didn't see Kirk and Co. steal the Enterprise, novelists would have probably blamed that one on Section 31 as well.