IMNSHO, Section 31 was probably one of the most idiotic concepts to ever be created for Trek.
a fundamentally silly concept(they're super-secret, so secret that they're off the books and no one knows of their existence. Think of modern technology NOW-how would an organization like that carry out its work undetected?), and moreover they're fundamentally unnecessary.
There's nothing Section 31 did that Starfleet Intelligence couldn't have done.