Perhaps it could be limited even further, to just the main planets of a House, Faction or perhaps important system. So Manhatten would be defended, but not Pittsburg. And Crete, but not Tripoli etc.
Besides, fighters would still be able to fight close to planetary defense systems. I dunno about you, but I can easily avoid toaster fire while still shooting my opponents. The defense system would really only keep cap ships out, and fighters on their toes. No one likes to be mobbed outside of their home planet by cap ships anyways. Shame on that Osiris, shooting at my poor Liberator outside Manhatten! Too bad he couldn't hit me =D