I think HTC should perk the carrier group. When someone takes control of the battle group, they are assuming responsibility for keeping such a valuable asset alive. Therefore the sinking of the CV under your command should entail a perk point cost to you.
On the plus side, the CV commander should get a graft in the form of a fraction of perk points earned by attacking aircraft operating off his battle group.
I think this would have a positive effect on gameplay. It should curtail the annoying occurance of players grabbing control of a battlegroup and then neglecting it. Players would be more attentive and cautious in the deployment of the battlegroups and not cheapen them into roving flak wagons to be parked casually off enemy coastlines when someone wants a few vultches.
