This kind of thing happens, provinces get destroyed, lots of people die, it's a common occurance
Okay, it actually isn't, but in a world where world threatening events have been known to ocurr and where the heroes sometimes have to kill
gods, it's hardly a surprise that this sort of thing would happen and some point. Besides, it happened to Morrowind, the Dunmer had it coming. And with the whole no emperor on the throne thing and all that, it's no surprise that other events that would change the status quo will also occur.
Maybe this is the real reason the Nerevarine went to Akavir, to save himself from the whole affair. Though I doubt that's the case,
As to how this will effect the series, for one thing, I doubt we'll see anymore games in Morrowind any time soon.