Jinn did technically tell them they had a choice to make, land behind bars or sign back up with the COG with full reinstatement of rank and all charges dropped… but also being pretty much pawns of Jinn.
We also don’t know when she found out about Kait’s Locust relation or about her going off to do her own thing despite JDs orders. Perhaps she understood that Kait having been at risk of turning to the Swarm was a danger that no one should’ve been willing to let persist, but then she is also crazy enough to try hooking Kait back up with the hivemind… so I’m uncertain. Perhaps Jinn didn’t find out at all but that seems very unlikely.