Here is a novel concept...try requiring escorts for battleships.
1 or 2 fighters are required to allow a battleship to move from one zone to another.
When the battleship has no escorts he is considered to be defending a particular area and can not leave that area to go chasing after a hostile.
If a clan has to dedicate 3 people to move a battlehip around you will see a serious reduction in the number of battleships flying around. This will eliminate mercs flying battleships as they will not have any escorts available to move the thing.
As to the comment about mercs not being able to get enough crewman together to crew a battleship, then based on that..how would they get enough to crew even a gunboat? So under this freelancer pilots merc, pirate or otherwise would be restricted to fighters due to crew limitations. On that note, there seems to be a lot of focus on griping about freelancer mercs flying around, what about the freelance pirates who are doing the same thing? Try to look at all aspects instead of focusing on the group that has been annoying you the most.