Sorry, my mistake. I initially thought my saboteur agent had rejoined the Empire, but that turns out not to be the case (which is fine by me; as long as she stays a saboteur, I don’t really care either way).
The choice I really didn’t like was the one marked as saboteur dialogue that doesn’t save the civilians. When I picked it, I didn’t know they could be saved and thought that option was the best that could be done. Then, when Theron was mad at the end, I had no idea why until I read that there was an option to save them.