Technically if the capship player in question does not do anything with his ship that would put it's resources in danger, then the faction cant do anything about it unless that ship enters a faction-owned guard system.
It's kinda like the deal with the rheinland military. If you decide to play an indy RM character in a gunboat/cruiser/whatever, as long as you do not set foot in braunschweigh and as long as you do not do anything OORP which would give an [RM] player reason to attack you, they cant do anything about it.
However, if the gunboat/cruiser/whatever decides to start firing at people without reason, he can be 'classified' as either psycho, rogue, or nomad-infested and destroyed on sight.