The only thing I can think of is he located a specific point in time that would allow most of the damage to be reversed, wiped out the Timelords and Daleks at that point, then locked it so no one could change it/prevent any possible paradoxes.
That's also what I've been thinking. He found a vulnerable point in time and did *something* that made the war a closed loop of time. It still happened, because we've seen plenty of alien folk mention it.
As for most of the universe being destroyed, I kinda took that to mean a whole lot of time travel fuckery. Like, "Oh shit, ceta alpha 9 is gonna be a massive loss for the Time Lords, I'll just pop back a few billion years and knock the proto-planet into the sun, problem solved!". And that shit would snowball, fast.
Random comments on the past two pages:
Jamie McKriven! He's the scottish dude who traveled with The Doctor, and he was a badass. "Daleks? I'll charge em with my little sheep skinning knife. MCKRIIIVEEEENNN!!!"
Brigadier is sadly gone, but they DID establish he had a daughter that was with UNIT as well. I'd like to see her come back.
Also, everyone keeps saying "Timothy Dalton". Does no one remember he was Rassilon? I really like the idea of one of the weeping time lords being matt smith. that would be a great touch.
Clara being Susan would be a cop-out imo. There's literally nothing in her story to suggest it, and quite a few things (leaf!) that suggest she was born on earth.
Anyone else think the magic-regeneration-drink could also make the number of remaining regenerations a wildcard? It could be any amount now, really. Though I am glad to have a 20 year mystery of the 8th doctor's regeneration solved. Jaw fuckin' dropped when I saw him.