There are still countries that aren't on the map yet, and the current map is the actual political map of the World. I don't see the sense in introducing native people until all countries are actually inducted in the game. Besides, what you're proposing would only fire up more disputes over ethnicity, occupation and past real history events that did not satisfy everyone.
It's true not all countries are on the map yet, and it could be hard to introduce countries that have few players but I think the goal IS to represent all countries when time is right and introduce more and more countries. To the rest I can just say that the world is not kind, it is cruel and the strong takes what it want both in world and the game, if you look at the world the strong don't care about the weaker countries. Look how most powerful military constellation use their power, to create wars everywhere and support facism instead of preventing it. I think it's wrong, but it's how the world works sadly.
What do you say about that one disputed region can have more than one "original region" then? This should be less discriminating because it gives both part in the game equal right to the land, even if they feel discriminated in the real world, for example Crimea to take a recent example and i can bring up more examples which has election to become free state this year according to same rights. To understand this you have to understand that NATO only support regimes that do as they say. If you don't, you get problem. Like Ukraine got where democratic government was overthrown and country cut all contact with their closest ally Russia and switched to opposite direction to EU/NATO even Russia offered 20 times better deal for Ukranian economy. However that is irrelevant now in real live politics, my point is that real world is not fair but it would be less discrimination with "disputed" areas in the game.