Both STI and STiD feature a rogue Starfleet Admiral with connections to Section 31 as an antagonist, although, in STI, the connection isn't actually made apparent the way it is in STiD.
Uh, Dougherty isn't rogue in STI. He's acting on orders from the Federation Council.
So he says. I see no reason to believe him.
Besides, the thing with the Ba'ku is exactly the sort of operation Section 31 would pull. The real Federation would never stoop that low. It's above that sort of thing.