Couldn't the permission system exist outside of the constraints of the in-game computer (as just some game mechanism)? If each of the ship's discrete components were accessible at some address, couldn't the game enforce the permissions at a level above the simulated CPU?
A rough static analysis of the code might reveal where those components are accessed, and as long as you enforce permissions while the software runs then you should be able to catch anything that tries to slip past.
Go back and look at the first post in this very thread. Notch explicitly intends nothing of the kind, and I certainly can't see why it would be done -- it runs counter to the vision thus far articulated.
A rough static analysis of the code might reveal where those components are accessed, and as long as you enforce permissions while the software runs then you should be able to catch anything that tries to slip past.