I'm talking thematically Section 31 doesn't fit within Star Trek outside of the morally ambiguous setting of DS9. It's made pretty clear that Section 31 is a rogue organisation that does what it wants without the consent or approval of Starfleet. Small numbers of rogue officers like in "The Undiscovered Country", "The Pegasus" and "Paradise Lost" do not represent Starfleet. The only time Starfleet does morally questionable things is in the event of war "In the Pale Moonlight", or when they're engaged in hostilities with another race "The Enterprise Incident". Also the Klingons having the Narada for 25 years isn't canon because it's from a deleted scene.