I get that this is a controversial topic, but here's my take on it (which IMO is still quite balanced).
If you manage to go through all the effort of saving your emissary flag from the dark abyss, I think you should be able to take it back to the faction you were an emissary of and then they'll give you the amount of gold you would've been paid if you had gone to them earlier and lowered the flag.
It's not much, but it would feel like less of a kick in the balls than only being able to sell it for 1 gold (as you currently can). And going through the effort of recovering it, I think you should get at least that much. Or if you still think it's too much, then what about half that?