Nothing need to be restricted, and no penalty should be added. The only thing, what should be made- another control pull. When offical faction has a control over it's indie capital fleet, and has GOOOOOOOOOOOD communication with it, (awesome, if few players are in both groupes, making something like bridge between fleets.) then there is no problem with it. Now, indies just laugh on fighter or bomber, who telling his capital ship what to do. Offical faction should have some pulls over indies. May be add another faction right, to downgrade ship. (with partrial refund?) In RP- ship's captain, was dismissed from commanding duty, or demoted. Something like that.
