Not necessarily. Even Slone may just be putting up such an appearance and may not be as 'evil' as he appears.
For all we know, Section 31 has the full backing and sanction of B(OTH the Federation government and Starfleet.
Why would Sloan have claimed to Bashir that Section 31 is not accountable to the Federation government if that were untrue? His goal in that scene was to recruit Bashir into Section 31, yet telling Bashir that S31 was a rogue organization produced the exact opposite result of his goal. He had no rational incentive to so claim this if it is a lie.
Furthermore, Section 31's status as a rogue organization was backed up in "Inter Arma Enim Silent Leges."
They are the IMPOSSIBLE MISSION FORCE (like the Desilu TV show that was produced and aired at the same time as the original Star Trek) of the Federation; and everything Slone has stated to non-Section 31 personnel allows Starfleet and the Federation to completely disavow and have complete and plausible deniability of their actions when they are exposed/caught.
Then why not just have them be a classified division of Starfleet Intelligence, answerable to the President and the chain of command but kept secret so as to be disavowed?
Also, if the Impossible Mission Force is truly a rogue agency that does not answer to the U.S. government, then Mission: Impossible is teaching us to idolize an anti-democratic criminal conspiracy.
The Federation and Starfleet have always done what they need to to protect themselves. In the 23rd century, we had teh events depicted in TOS S3 - "The Enterprise Incident" - where Captain Kirk was setup as the 'fall guy if things went bad:
^^^
So then, Kirk and Spock are 'evil' too...got it.![]()
Kirk and Spock were still part of the chain of command and still answerable to the democratically-elected government of the Federation.