Earlier quoted context omitted.
I was thinking they could treat software and components like we do when granting third-parties permission to access our Twitter/Facebook accounts: Plasma Shield Generator requests the following permissions: * Read/write to the ship's log * Draw power from the core * Use the red alert system Plasma Shield Generator will not: * Access communication protocols
It's 128KB of RAM, that's the same as the original Macintosh in 1984. I would be surprised if it ran at more than about 10MHz. And nevermind the constrained resources for implementing any of this hypothetical infrastructure, unless Notch adds an MMU, you can't enforce permissions You can't think about this in modern terms. It's not a modern computer. It's a 1980s computer, and it's supposed to run a spaceship. Think…
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.