The answer to one big problem in Star Trek: Section 31 is found in the return of Captain Worf (Michael Dorn) in Star Trek: Picard. As part of Star Trek: Picard season 3's Star Trek: The Next Generation cast reunion, Commander Raffi Musiker's (Michelle Hurd) mysterious handler is revealed to be none other than Captain Worf. Commander Musiker assumes that Worf is also working for Starfleet Intelligence, but Worf explains that he's more of an "independent contractor." Given Worf's long history with both Starfleet and the Klingon Empire, this unites Worf's loyalties with one job.
Ever since being introduced in Star Trek: Deep Space Nine, Section 31 has been different from Starfleet Intelligence. While Starfleet Intelligence is the Federation's standard espionage division, Section 31 was a black ops intelligence team that didn't answer to Starfleet Command, and wasn't bound by the Federation's code of ethics. As a refugee from the Mirror Universe, Michelle Yeoh's Terran Emperor Philippa Georgiou was a perfect candidate to join Section 31 in Star Trek: Discovery season 2. One big problem in Star Trek: Section 31 is that Georgiou's new team doesn't have that morally gray nuance.
Section 31's Team Of Misfits Could Have Been Star Trek Independent Contractors (Like Worf)
Once Again, A Star Trek That's Improved By Worf (Sort Of)
The team of misfits in Star Trek: Section 31 could have been independent contractors, like Captain Worf is in Star Trek: Picard. It's unclear why Alok Sahar's (Omar Hardwick) team in Section 31 actually has to be Section 31 at all when their mission isn't as morally gray as Section 31 typically is. Lieutenant Rachel Garrett (Kacey Rohl) is even there to ensure that they don't kill anyone. But Worf's job in Picard season 3 proves that Starfleet Intelligence does use operatives who don't work for them directly and aren't necessarily bound by strict Federation ethics.
Making Section 31's team independent contractors would solve one of Star Trek: Section 31's problems: its unexpected tone. Star Trek established that Section 31 operates in the shadows of Federation ethics, even when Section 31 is an open secret in Star Trek: Discovery. Instead of being morally gray characters on ethically dubious missions, Star Trek: Section 31's team are more like Star Trek superheroes. If the Section 31 team doesn't actually operate like elite black ops, they should be independent hires for specific missions—then they can be as fun as Star Trek: Section 31 made them out to be.