This sounds so familiar! "The previous local populations just vanished and we, the current inhabitants, had nothing to do with it, cross my heart!"
The dramatic change should have been very beneficial to the hunter-gatherers. They survived so long in tundra but they somehow couldn't cope with the abundance of plants and plant eating venison brought along? Come on! It's more likely that the previous harsh conditions weren't that inviting for the better hunters of N type super-haplogroup living somewhere else, and as soon as that changed so did the hunting lands' owners!
In fact, this is so inevitable we'd have to explain why it couldn't happen, before speculating on less-likely scenarios?
The colonization of Americas is the perfect counter-example for disease wipe-out explanation. Pre-Columbian American population had no immunity whatsoever to a bunch of serious diseases (some of which managed to become pandemics back in colonizer's homelands), diseases that have accumulated over millennia (since the last Bering overland/over-ice human crossing)! You'd expect that on first Columbian contacts there should have appeared a pandemic so severe over the whole Americas that after a few years the Europeans should have had no one alive to encounter! Not only they still encountered, but long after the first contact they also had a hard time dealing with local resistance of underdeveloped tribes which had worse medical conditions than what was to be had in ancient Rome! Not only that locals haven't been wiped out, but they managed to contribute in a large quote to nowadays's Ibero-America's genotype despite the European settlers' massive migration! So yes, I think it's enough reason to consider the disease a less likely cause for a continental scale wipe-out (which is what the article was talking about).
We'll never really know the depth of native culture pre-Columbian because of this.
Could this more easily be explained by an aggressive disease or plague that wiped out anyone it contacted and the separation of the 2 groups (N and M) in different locations protected enough of the N group for it to prosper. Also isolated pockets of M carriers who had migrated beyond the infected area survived.