He has bigger guns. The only way that a faction can control these things is by using their own power, which is how it is in real life anyway.
If a civilian refuses to obey the law, they get put in jail.
If many civilians refuse to obey the law, they all get put in jail but questions are asked.
If a hell of a lot of civilians refuse to obey the law then things can get very violent, especially in countries that allow civilians to have weaponry.
My point is that It is Up to the FACTIONS to control the ships. Not the admins. If you can't control them then you hardly deserve to RP as the entire faction.
The only time that Admins should become involved is when there are unfair or unjust things happening. Favouritism is not included in this since a faction is hardly going to give a ship to someone they don't like.
Simple solution to the bomber issue, up the hull/shields on all capital ships.
Trade route wise. Make some RP routes that pay well. The only reason people do the OORP routes is to get the extra money. It isn't exactly OORP to do the Diamond - Niobium run anyway if you are a freelance trader.