The reason the ability to FR5 players with the same ID as the official faction no longer exists is that it ended up with the kind of ships/character that antagonise Spire so greatly.
I'll use an example to elaborate. This is by no means a criticism of either faction involved, just a demonstration.
TCG got into fights with Order|. Order| FR5'd TCG. Then, TCG could no longer dock on Order bases, yet they still had Order ID'd, Order ships, with Order guns. Problem?
Therefore, FR5 is not effective and creates a sort of paradox in this situation. Hence, one must resort to a 6.9 sanction, in which the offending player must be punished for not following the ID.
Therefore, the only solution is to file for more 6.9s, or introduce a Faction Right which permits an official faction to kick a player out of the NPC faction entirely, both repping them hostile and removing the faction ID (swapping it for the most appropriate generic ID). However, I highly doubt the Admins would even consider letting official factions have that kind of power, thus allowing players not interested in joining a player faction to be able to join the NPC faction. However, when an "independent" goes rogue, so to speak, an official faction has little power to bring the player back in line because the offenders will often not recognise or acknowledge Faction Right 2. Therefore, the only remaining choice is to file for a violation of 6.9.
When it comes down to it, rule violation reports are the only effective option for stubborn players. It's a terrible shame that the reporting system is slow and frustrating for many since it's difficult to know if your report has been acknowledged and/or processed.