If a city is meant to be destroyed in Skyrim then so be it. If you want to rebuild it you can always create a mod like they did with Kvatch.
Why would you want a city to be permanently inaccessible? I s'pose you enjoyed the smoldering wreck of Kvatch, never to go there again?
"blah blah blah get a mod to fix it"
No. Why should I have to rely on someone else to do the job BGS couldn't? Anyway, I have no doubt there will be recuperation of cities, especially after what they did with Kvatch, they wouldn't do it again.