Where are you getting this idea that the Pre Rune War inhabitants of the Kumungu were inferior primitives caught in the war between two more developed foreign nations? The Lore of the Rune Wars lacks detail, but we have no reason to assume that these people we not just as advanced both technologically and magically as their enemies just because they lived in a jungle, and there is nothing to indicate that they were not involved in the Rune Wars of their own volition.
I didn't say inferior primitives because I don't think less technologically developed people are either of those things, but I think some people might see it that way. I figure that since Ionia (the easternmost part of Runeterra) is inspired by a lot of Asian culture, Demacia (the western part) is inspired by a lot of European fuedalism, and Shurima (the desert part) is inspired by the middle-east, LoL players are going to assume that Kumungu (the jungle) is inspired by the Amazon/Congo/Southeast Asia. In which case I think it wouldn't be responsible to make those people extinct with no explanation. Especially since we do have champions from that area, but they are all animals.
Why weren't the animals driven out by the Rune Wars? The existing storyline reads to reinforce the idea of jungles as too dangerous for people, which isn't true at all. If every other part of Valoran gets to have a human population (even Zaun and Kalamanda -- which were also both probably pretty scarred from dark magics), I don't see why Kumungu doesn't get to have a human population too.