Yea, a while ago we put in the logic for the AI to automatically retreat all its "civilian" ships (engineers and rebuilders, etc) to friendly worlds so they don't clog stuff up, but the stationary stealth tachyon emitters...
Unless someone thinks they're a legitimate and fun challenge, I think some way of getting those inoperative AI defenses to go away with or shortly after the command station would be a good thing. I think I'd have to restrict it to "no command station and no supply", though, since there's a lot of requests for AI-recolonization and if they recolonize a border world with a lot of turrets still there they would be useful again.