The scenario in Greg Cox's Eugenics Wars novels would be an ideal way to resolve the situation. Unfortunately, ENT more-or-less trampled that when they gave a death toll numbering in the tens of millions; far more than was portrayed in the novels. As bad as the conflicts in the books were, nowhere near that many died. That's the biggest obstacle to accepting Cox's account.
I don't think there's a real problem with that. I mean, hell, something between two and five million people died as a result of the Second Congo War
in real life, but you'd never know it from watching American media. Those books are essentially built on the disjuncture between American perceptions and actual reality; one could easily say that many millions more are dying in Africa as a result of the Augments than the main characters are even realizing.
The number of people killed in wars in the 1990s is still nowhere near the figure given in ENT though. And where did all those Augment embryos come from? I'd think any left by Chrysalis in the 70s would have been destroyed once their operation was shut down by Gary Seven, and as I recall, none of the Augments were able to replicate their success in the books.