For the same in-RP reasons that you presented that the Coalition does not have indies I could provide a number of them for other factions to not have them as well. Do you think the Order has indies in-RP, for example? No, I don't think they should, due to the nature of their group. There also should not be Gebs parking Ainu looking for revenge kills because we killed their traders.
The Congress may not be the Junkers as a whole, but we are the ones who represent them. For the same reason that you said it would be impossible for coalition indies to appear I could forward that there are no Junkers with the mentality of power-pirates or that parade themselves with contraband in front of the police authorities ( all of which go against cannon RP, may I add). In-RP we would find them and lock them away until they started behaving in a way that wouldn't damage Junker reputation. Does that mean that we can restrict the Junker ID as well?
You assume from the start that all people that don't fall under the original Coalition are idiots? Nice mentality you have there, really... Take the Jackal Wing, for example. It does not fall under the usual Junker RP, yet it provides great RP encounters, going where Junkers usually wouldn't dare. By shutting down indies you aren't just killing idiots, you are killing idiots and possible great RPers, hence killing potential. Heck, when I first came to disco I was a complete jackass with a Red Hessian Cruiser with a Rogue tag and Outcast weapons, see what I have achieved in one year.
I have whacked my share of idiots as well, believe me (not directly, of course, I just payed someone off to kill them, or else it would be OORP) but as old as it can get it is one of those things that we are obliged to do as official faction members. As it stands now, I feel that the Coalition is getting special treatment.
I already gave up on this matter, though. After some chatting on skype it seems that the communities mentality is already deeply carved in place.