Maybe instead of making them hostile, commissions could just make enemies inhospitable if you haven't actively antaged them. Maybe you could add some exceptions (joining eos makes templars vengeful) but in general it's just inhospitable.
Seriously I think the commission system was designed with only four major factions in mind, do you want to fight for the tachyons, the hegemony, the pirates or independents. When you've got 15 factions with a web of relations the antaging can get...ridiculous. Moroever, becasue factions don't just control fleet types and markets but also whole quadrants then comissions can be...limiting, especially near the beginning. This isn't really a balancing issue so much as a fun issue, I like being able to cruise around the expanded galaxy and read all the cool descriptions and buy neat things, if half the galaxy hates you that's lame. Of course eventually you do want to antag everyone and destroy the galaxy as an endgame, but it would be beter to do that piecewise than all at once.
Granted you can just avoid comissions (which I have been doing) but perhaps this problem is just related to the fact that it's really hard to make money through fighting alone right now between crew and supply costs, bounty difficulties/competition with AI, and with commissions makign the game into a gauntlet it's just logisitcally frustrating. maybe that will change with the next build.
