Spire here isn't talking about removing all indies. What he is aiming for is to stop the incessant lolwuttery of certain indies. His example stated is an indie claiming he is not part of a particular faction and is a full independent despite having said faction's ID and IFF, all for the sake of pirating without a nerf.
We shouldn't remove indies, we should just have a tighter hold on them. At least implement a faction right that allows the sanctioning of indies within an NPC faction. I would prefer that FR5s can be applied to indies within the same faction. This way, any person who goes around shooting his own men can be branded a "traitor" and be FR5d, thus preventing overall lolwuttery.