"ohhhh but how would they go about season 2 when there's several different endings??"
Guys. Season 2 starts with Robert having a meeting with HR and it's gonna be like:
"So the SDN member that went rouge, uh..."
Like they can easily just ask about your decisions like they did in The Witcher 3. And then build on that. Whether or not you sent Sonar/Coupé to prison they end up back as SDN anyways - after all, it's a program for Ex-criminals!
Visi keeping connections with the Red Ring works for both her endings - either she's working undercover or she's with them but feeding information to SDN.
Anyway, I think there's a lot of ways to write around the issue. I'm sure they'll come up with something.