It sounds like a cool idea, and could expand into a lot of cooler ideas as the game itself improves. What if you're friendly with a merc group but end up in a war with them? Or maybe you're a high-ranking hedgemony officer and buddy-buddy with some high ranking mercs, so they're more willing to offer better prices to the hedgemony.
It'd also offer a way to see a lot of the game even if you're sticking to a single faction - if you're part of a merc group, you'll get to fight alongside, for and against various sides as the game progresses. If you're part of a faction, on the same note, you'll fight for and against various merc groups depending on how the game goes.
I consider it a mild weakness of the game that, by joining the Hedgemony, you never get to experience what it's like to fight alongside Tri-Tachyon against Hedgemony - at least, not in that file. The closest you could get is capturing TriTach ships and going after a rebel hedgemony bounty - which is quite rare.
It sounds like a good idea both in terms of what an individual player will experience and for expanding the game-world.