so UH, wtf was the point of that story? to give a girl an awful childhood with an abusive father? great job. i feel really satisfied with that ending....
More BSI spoilers, I guess.
She stops all the deaths that Comstock's survival would've caused. Everything that Columbia attacked, everyone that died in the uprising on Columbia, everyone that died when Elizabeth took control. All of that suffering and death didn't/doesn't happen, now.
Plus the Stormcloak war has been going on much longer then the events of the game suggest. At the point you come into the game the war had been going on some time, with the Tharalmor aiming to prolong it by it's timely interfearance by taking people to cull for Talos worship. The result of the war is of little interest to them, just the longer it goes on for, the weaker the empire would be.
And there is merits to rebellion. Hammerfell resisted furiously and managed to drive out the Dominon single handledly without the empires assistance. Personally I joined the stormcloaks out of purely selfish reasons to have my hand in my own empire, as I know full well that I as dragonborn could drive out the armies of either.