The reason why capital ships are in guard systems is so that people can't get the ships unless they are at least friendly with their NPC guard faction. Thus you don't get Hessians grabbing Rheinland Battleships (Usually).
It makes it harder for people to get these 'all powerful' ships basically.
It doesn't mean the player faction can restrict complete docking rights etc. Considering that player factions may not be the entire NPC faction, that just makes common sense.
However, if stations were made to be player faction specific (IE, a shipyard that is only for the RoS) then proper rules could be brought in to allow the RoS to enforce their laws in regards to that station and what it contains.
However it would mean that non-player faction specific ships would have to be contained at NPC faction guard bases that are not player faction controlled.
Overall however, having certain stations as player faction specific might solve a lot of these issues.
