April 24, 2014 2:11 PM EDT
The Last Dragonborn, if you're going by where the story line leads you, would side with Whiterun, and unless you push Balgruuf, he will stay Neutral.
The Last Dragonborn is above the selfish squabbling rebellion, becoming Harbinger of the Companions quickly, and once Alduin and Miraak are defeated, I like to imagine he makes a peace treaty with both sides, and leads the attack on the Thalmor with a host of Dragons, Blades, and an united army of Men.