This is an interesting question. First, in the dojang where I train we used to have Korea and Brazil's flags, I don't remember wich in right or left, but I never cared about the position issue. About a year ago the flags were put out. I believed it was due to some repairs they were making in the painting, but the flags were not held back since then. Anyway, I'm sure in my city (and probably in my country) the dojangs usually have both flags, and it's a custom to salute both of them (here both at once).
I think it should be okay to have the Korean flag, once taekwondo's origins are set in Korea, but then... hey! I think: so why wouldn't we hang Japanese flag, too, due to the important influence of karate in taekwondo? Or maybe we should hang Okinawa's flag, or else Chinese flag, because of Chinese martial arts in karate (and maybe even directly in taekwondo). Thinking about this makes me believe the "it's country origin of the martial art" be not enough a reason. Anyway, I think it's okay to accept the reason: "it's where taekwondo was brought from to us". To me it sounds like a nice reason to hang and salute the Korean flag, then.
Maybe the Korean flag custom comes from military relations in taekwondo's foundation history, or from some kind of guidelines received by the pioneers before having gone to foreign countries. I think to discuss where this custom comes from would be as important as for why the flag should be held in the dojangs. Does anyone know about it?
Finally, despite some kind of tendency of taekwondo becoming more universal, which I think is ok, I also believe it's good to keep a large part of tradition, so the martial art would remain as we recognize it, and the way it was shown us as a good thing. So to keep the tradition seems another good reason, in my opinion, to hold the Korean flag on the wall of the dojang.