Stupid newbie, but how about this; Folk simply can't buy a capital ship.
They can get them, though, in the same sort of way people get barges, apparently. Save in this case their faction leads give it out or at least a GM would give it out for faction leaders. For the sake using a example that I actively know about, the SCRA| lads only allow people of a certain rank to be able to use capital ships. Why not the same thing, here?
Now, granted, there will probably be a fair amount of favoritism and it might get a bit mucked up if (player) faction leads kinda stop paying attention and of course people with the ships would kinda be prompted to do it, but it ought to make capital ships more... Well, capital ships.
And, of course, people who want to play as a Cap' would probably kind get left in the dust. And I could see the necessity of buffing up Caps to compensate for the fact that there isn't so many of them and there doesn't need to be a way for a fighter to be able to down one.
Gunboats might still be available, though, to allow people at least a taste of it. Free Frigates/destroyers for all. But cruisers, carriers and battleships? Only for the white hats.
(Edit: And, of course... People... Would have to lose their ships...)