Personally I don't see what the problem with the Gunboats and stuff being in the core systems. I don't even have a problem with the cruisers, those can be taken out too with a little acuity.
Perhaps the BHG player faction should take steps to restrict their capital ships in-RP, such as the Rhienland Military and 101st have done with theirs. That way there wouldn't be so many indies running amok in their big ships.