I think the bigger problem is that you can dock with all kinds of funny stuff like an orb (orb base is it?). Well I say you can, you can get your docking computer to take you in, but it crashed me the time I tried it, not sure if you can get a little ship in the gap. Or a Rock Hermit pirate will still let you dock whilst launching ships to attack you (as long as you dont crash on the way in)
Maybe a better solution would be to have the docking place have two types, an NPC-dock and a player-dock, kind of like there are differrent types of ships? Or give them a role (open|closed).
Then you could set up oxp however the author wants, so thargoids are not dockable (presumably, although, maybe you could have a mission with a renegade, or a nicked one or something?) and other stuff like the behemoth is dockable.