“Illegal?” DS9’s S31 was protected by Starfleet Command. They were completely untouchable.
They can be both protected and illegal. Sisko noted that the organization was completely antithetical to the laws of Starfleet, e.g. committing genocide against the Changlings of the Dominion (they used the actual word “genocide” to describe what Section 31 did in the show). But their existence was neither denied nor acknowledged by Starfleet. This is part of the reason why he asked Bashir to act as a double-agent.
It was clearly analogous to the CIA, which for decades has been collecting money from the illegal drug trade and supporting terrorist organizations around the world, all in the name of “national security.” It was a critique of the US government, like most of the Star Trek episodes that deal with the moral shades of gray within the laws of Starfleet. It is clear from their political commentary that the shows morality was staunchly anti-fascist.
And this new film on Section 31 completely reversing their former politics and joining with and celebrating the fascists is more than I can stomach.