Perhaps provide an option to buy Task Force Mission time for $$$ perks.
Anyone who coughs up the perks immediately assumes command over anyone else who has not paid, no matter what the rank. When a Task Force is in a "paid-for" mission, no one else can hijack it. Presumably people who pay for a Task Force mission would want to accomplish a mission - probably great for squads or joint squad ops.
Make the CV perk loss price equal to the perk price of an airbase. If you take a base but lose the CV, the Task Force commander breaks even. If you take a base and all vessels are in tact, woo hoo, you clean house.
Lesser vessels are less of a perk loss. Ports could be something a bit less valuable than an airbase, as could Vehicle bases.
Planes, PT boats and LTVs are the individual's responsibility, and if downed are not counted against the Task Force commander.
Best.