I look upon factions as the official voice & indies as perhaps more maverick agents. I have often seen both working together and other times 1 or 2 doing their own thing. As long as they are working for a common purpose I see no problem here. If as Fletcher points out, players are treated disrespectfully then its all gonna go Pete Tong & where's your moral highground gone? Its a game not real life.
I work in Accounts & hate writing off debt, my colleague doesn't care if it makes the records tidier; this brings us into conflict, but 95% of the time we work for a common goal. I work for the company, he is a temp. I am part of a structured organisation, he works for an agency (an indie so to speak) - but if he doesn't work hard with me he's out on his ear. The parallels between Freelancer & real life aren't too dissimilar. If the indies work (or semi-work) with the factions I cannot see an issue. If they put 2 fingers up at the factions then they deserve what they get.