As far as I know gencores and kdys haven't really helped me in protecting a system from espionage and sabotage, only from orbital bombardment. Did any of the people from the rebellion, including Han have the ability to use the force? In a situation like that, it seems odd that your opponent would be able to do that. Was this sector a core sector or an outer rim? Did you have enough time to bring in other ships and an interdictor cruiser to obliterate and capture the lone rebel ship? From my experience it takes quite a bit of time to destroy every storm trooper, and mine and refinery, as I play the rebellion most of the time. I have tried this before, and more often then not my opponent will send in a couple of ships to either drive me off, or destroy and capture my characters. Another thing that actually helps is to have imperial commandos on those worlds in which you don't have fighters. That is what I do from time to time to prevent the destruction of my mines and refineries in a system.