Well the Empire started in Skyrim. All Imperials and the Empire we know today all descended from Talos, or Tiber Septim if you wish to call him that, and his Nord army. If the Stormcloaks beat the Empire, they'll just become the new Empire, and likely the Dragonborn will become the Emperor. People assume that the Thalmor are an undefeatable fighting force with unlimited numbers at their side. This is not the case. If the Empire were to rebuild it's armies, or if the Stormcloaks formed an army to rival the Empire's, and marched, or rather sailed, into the Summerset Isles, they would decimate the elves. The Imperial Legions already decimated Thalmor armies in the Great War, so they could do it again, as could the Stormcloaks. Even more so with a Dragonborn emperor at their side, and even more so if the Dragonborn went to the Temple of the One to light the Dragonfires. Besides, it honestly doesn't matter who wins the war, It is stated in a dossier you find in
Spoiler the MQ that the Thalmor want the Civil War to continue. Either side winning is bad for them, as a united free Skyrim is just as dangerous to them as a strengthened Empire is.
Also, and this is just stating a silly little fact, the Dragonborn has the power to call in a [censored] dragon with a shout. A. [censored]. Dragon. That dragon could likely destroy an entire Thalmor army itself.