Add a seperate perk category for this, and they have to earn X amount of perks in the gun to be able to command a CV. If a person sinks a ship while they are in command, they lose perks. Varying on Destroyer, Cruiser, and CV, destroyers would be X amount of perks lost, up to the CV.
This would do 2 things:
1.) Enable more ship defense, not just taking command and letting it roam free
2.) You have to work toward commanding a ship.