I think the problems here is how factions are handled.
They are rather clans than factions. A real-life faction can have many sub-factions united under one president or any other government.
And even military leaders are not permitted to kill annoying civil reporters just for fun.
I think we don't need a perfect permission-system, just one to match the real world more.
Thiefs -even faction members- should be able to break it, but there should always -dependent on design- be a risk of losing reputation or triggering a trap.
A person should at least be able to
- add a named permission rule-set to a ship
- include other rule-sets as defaults for this rule-set (white-listed (1) + black-listed (-1.5) = -0.5 = negative = forbidden ?) with restricted possible permissions.
- include a faction rule-set with restricted possible permissions.
Link different ship areas or computers to different rule-sets (such as doors which auto-close after a few seconds, etc).
Somebody could be allowed to enter small weapon computers, but not the main weapon computer for example.