I think they've written themselves into a dramatic hole. I'm sure they thought it would provide a feel good ending to have Seven and Raffi side by side. Going forward: (1) there is no dramatic tension between the two, and Raffi is just a mouthpiece for Seven; (2) the drama will make their relationship unsustainable; or (3) Raffi is not longer part of Seven's command hierarchy. IMO, 3 is the best option. Raffi might be a recurring character, the working woman who doesn't live with her spouse, being on special missions. Maybe she commands the MACOS, being on the ship but separate. I suspect they'll choose 2.