If it could really be done I'd say have admins control capship purchasing, but a third party -has- to be there. The admins dont have enough time or patience to deal with every person who wants to use a capship - the factions can intermediate and monitor a player in-game to see if they're responsible enough to use the capship, and then allow them to purchase it.
It's the same deal right now with players who want to be phantoms, keepers, or wilde characters. The admins have to make the rep change, but they cant watch every player in the game who wants to join those groups - so the factions who run those groups are the ones who decide who joins and who doesnt, after observing their behavior in-game.