If the fleet's rules are to only use canon/faction-affiliated ships in group events, then that's the fleet's prerogative. If you don't agree with those rules, don't join that fleet. It's no different then a fleet requiring a specific fleet uniform..
But to use that fleets prerogative as reasoning to not make the ship a lock-box item? Come on now! I have to call the Whaaaaaaambulance on situations like that!