Neither will be canon. We'll never hear who won this war in future TES games. The Thalmor would have invaded and crushed whatever fledgling peace springs forth in short order. To avoid another Warp in the West, Beth has to make it so the world won't know or care who won this war 200 years from now.
My guess has always been that whichever side wins the Civil war eventually takes the fight to the Thalmor (most likely in a future expansion), and wins. However, no matter what happens, as a result of prolonged war and what has been a very long decline since the end of the Septim Dynasty, the Empire buckles.
In the resulting chaos, whoever won the civil war in Skyrim becomes lost to the sands of time.