Frontier can consider building a simple rights system where you can delegate which modules can be used by whom. Regardless, the ship's CMDR can actually simply disable modules such as SCB and HSL so they are unable to be used; crew cannot enable/ disable modules.
The method to control access, albeit rather coarse, already exists. Really that should be entirely sufficient. It seems very evident that this isn't really a problem with rogue crew, it's hosting commanders who simply haven't thought about what they are doing.
Frontier can't fix that.