Or maybe after a year or so they could at least stop burning.
That's certainly true, while buildings would only be rebuilt if someone made an effort to rebuild them fires would eventually burn out naturally even if no one put them out.
But I agree that if any cities get destroyed during Skyrim's storyline, they should get rebuilt after a while, not suddenly rebuilt after the main quest is completed, but gradually rebuilt as time passes or if the story requires that they stay destroyed for a time they can get rebuilt as you progress through the story, so you get the rebuilding effort progresses over time feel but the developers can still make sure they don't get rebuilt when they still need to be ruins. Cities shouldn't need you to help to be rebuilt either, after all, you're job is to slay dragons, not build cities, though there could be an optional questline where you can help with the rebuilding effort in some way, I suppose, maybe by helping the people get materials needed for the proccess or finding people to help with the project or something, doing these quests could make the place get rebuilt more quickly, but it could still be rebuilt without your help.