There is no need to urge people to registrations in my opinion. Reason is simple. Keeping a track of it will get immensely hard at one point in major houses such as Liberty and others. Actually what I tell here should be viable and sufficient for all groups trying to concentrate on dealing with undesired actions, the independents cause. Blaming the independents as a whole won't remedy anything but irritate the fuss worse at the first place.
In short, what I would suggest is to coordinate your factions on which actions to take against undesired situations once they occur. Warn your own folk how to act when such a case occurs. Have an operation manual and distribute it on secure channels. Also let your actions be known on forums so that people could or at least try to be acquainted with them in time. Use the tools of roleplay and do what a reasonable officer, leader or whatever would do. Be sensitive and objective at this point. Is a capital ship creating trouble or anything undesired for the dominant lawful faction in their ZOI? Deal it within RP then, board the vessel or force it out of the system. Levy it a fine, dismantle it to scrap metal as a last resort if the person in question is reluctant to participate in what the reasonable roleplay actions would require to do.
Remember, they can't whine or validate their arguments with which they attempt to accuse you as long as you are reasonable in your acts of roleplay.
On the uncharted lagoons of anguish, I sail with a canoe made of my sins.
