Yeah, I don't think I ever thought about it before but in a way it's kind of a weird line since they seem to have quite a bit of autonomy so as to not be government lapdogs and even have held out on very rare occasion, but perhaps they still are. Also, after 2nd Gig she kind of does leave Section 9 for a while to work on her own, until that SAC: Solid State Society movie.
Arise, the AU prequel, also brings up again that part of Motoko's terms for agreeing to Aramaki's plans for Section 9 was in regards to the amount of autonomy her team would have.