This whole thread has me chuckling
How on earth do the independents manage to keep trade going and not have a faction spontaneously declare war on them, because they might happen to prefer trading with the faction that is willing to pay more for their cargo?
Oh...paying off these investigators..
I think bounties and trading with factions should not affect your standing significantly with factions, since these services are a good thing for everyone and a necessity in the sector. What should affect your standing is missions that are actually aimed at changing the faction power balance in the sector. For example: 'attack the Hegemony patrol', 'disrupt trade', 'steal experimental tech from the Tri-Tachyon's' etc.
I have a strong suspicion that this is actually where these massive reputation penalties are planning on being used, and Alex is just trying out the mechanic with the basic quest system implemented as it is; and I would laugh hysterically about it if it wasn't for the fact I will probably never be the owner of a Paragon in my playthrough (Damn Tri-Tachyon investigator).
There is one independent planet that sells pretty good stuff (They have an independent military tab to sell ships), Planet Nortia in Askonia...perhaps I might get lucky as they have sold Tri-Tachyon stuff before.