Mr. Laser Beam wrote:
Section 31 derives its (supposed) legitimacy from Article 14, Section 31 of the Starfleet charter. But the thing is, it's the Earth Starfleet charter, not the Federation Starfleet. So in a very real sense, Section 31 lost all claims to legitimacy when the Federation was formed, since the two Starfleets are not the same organization.
We don't know that the Earth Starfleet charter wasn't then used as a guide to Federation Starfleet's charter. We know that a ton of facets of Earth Starfleet (rank structure, starship design, etc) were integrated into Federation Starfleet. Who is to say that Section 31 didn't also make the cut?