That svcks. I'll probably not do the civil war campaign at all in this playthrough then.
At least don't do it until you're towards the end of your character. I learned the hard way that doing the Civil War quest early on has disastrous implications in terms of breaking other quests. For instance, if you join the Companions after the Civil War and they give you the Hired Muscle quest, you're screwed. The reason is because the guy you have to intimidate lived in one of the houses that got destroyed and he no longer exists. Therefore you can't play the Companions quest line.
Also, it wreaks havoc on the MQ. I'm pretty sure that's the reason I can't further the MQ anymore. Either that or don't become master of the TG before finishing the MQ. Bugs galore.