I suppose this would make people happier with the Civil War in the next game. Some people want Stormcloaks to rule, others want the Empire. Well, what if after all the conflict, the country is just split into two different states, probably not even Skyrim, anymore. I have no doubt that the Stormcloak side would keep the 'Skyrim' name, but I could see the Empire changing the name of their half of what was once Skyrim.
Honestly, I can't find another way of making the Civil War a moot point in the future of the Elder Scrolls, besides not at all mentioning it, which would be silly...