Does resolving the civil war make areas inaccessible?
Solution 1:
The only major difference after a town is captured is that the Jarl will change (Solitude is an exception to this).
There is no need to worry about your house, potential quests, or followers - the only casualties of war (aside from Tullius / Ulfric) are nameless "Imperial / Stormcloak Soldier"s. The Dohvakiin is unaffected.
Solution 2:
It's worth noting that some NPC houses (such as Heimskr's) may be inaccessible after battles have been fought in their towns. Therefore, certain random quests that require access to them may be bugged.