Well, we probably couldn't interbreed with Neandertals anyway, so they never were human, and peaceful coexistence with them wouldn't have added to our genetic diversity.
Chimps also have much more genetic diversity within their species than humans do in ours. But both species wage war among themselves. It's just that humans migrate all around the world, while chimps stay in their own isolated regions. IIRC there are at least 3 separate areas in Africa where you find chimps - one of which was only discovered a couple years ago. And this is not counting bonobos, who split from regular chimps into their own species.
If a human generation is 20 years, then for a human population to be genetically isolated for 50 generations that would take 1,000 years! I don't think that any group of Homo sapiens were ever isolated from their neighbors for that long. So any mutations that took over a single population would eventually find their way into many other populations before enough mutations were able to build up between any two populations to make them separate species.
Does that mean they didn't have "souls", what ever those are?
If we had bred with them, would that have changed?
How about Australian aborigines or American natives?