Apparently without me being involved in the quest my good buddies the Stormcloaks had decided to go on and wreck the place for me ahead of schedule. While I understand this is probably what would happen if the army did indeed walk on foot there over time I'm peeved as I had figured it would be a point of no return. Now the Companion Questline amongst other quests will forever remain unfinished.

Based on my experience doing it the other way, waiting until reaching a relatively high level before joining the Civil War and being powerful enough to two-shot Ulfric if he wasn't immune to death, promptly slaughtering the entire city guard and getting a 15000 bounty on my head, then later winning the war and having my bounty rendered void and the guard being replaced with Imperial Soldiers:

Once you actually complete the quest chain, you should regain the use of former enemy cities under new leadership.

Hmm I'd heard that some things in the cities got wrecked in the battle killing a number of the inhabitants, I was led to believe that the companions questline would be uncompletable.