Gameplay > Concept > Realism.
Doesn't matter if it's realistic. Games are heavily abstracted, not a simulation of reality. The gameplay requires that there be discrete factions, and that your actions with one influence standing with that faction directly, and possibly other factions as well. Too much granularity on this level would simply be noise. The game wants to model complexity on the loadout screen and ship systems, not its fictional politics.
If one wants to diminish the impact of your actions through anonymity, the game provides the transponder mechanic for that.
I don't get what the problem with Independents is supposed to be. It's just a label. The only mechanic is the shared standing, and that makes total sense.
If the independents were a bunch of sub factions they'd still talk to each other, at least if someone is either hunting them down or helping them out a lot. So you'd have to implement the same shared-standing mechanic we have now, except maybe for a little 0.X multiplier to simulate mitigated impact of your actions on other independent sub-factions.
I agree with gameplay > realism but the independent faction system atm is just a copy paste from the rest of the factions. It feels unfinished/like a placeholder. It's ok for now but I would expect something more for the finished game. I mean the Persean league is what the Independents feel to be now, independent worlds allied into a single faction. A 0.X multiplier would be a good start to change that feeling.
Furthermore the transponder mechanic is fine for the core worlds but with the addition of the outer rim I think it isn't sufficient enough anymore. You are far off in a corner of the map and see a scavenger go pirate switching his transponder the way it's convenient. In one moment Pirate in the other Independent and vice versa. If you then attack an Independent, several tanker loads away from civilization, with transponder off no less you get an instant reputation loss with an "Independent faction". That just feels bad and destroys immersion.
I'm not saying you should be able to attack everyone without repercussions but with the new additions in 0.8, in my opinion we should have a discussion about faction interaction and transponder mechanics in conjunction with the new systems.