Civil wars can be like that - see also the history of the English civil war, where you end up with "Roundheads: right but repulsive; Cavaliers: Wrong but Romantic".

I think if you're going to find a way to not be ETERNALLY at that civil war, until it's not really a civil war anymore it's just a war over a specific bit of territory, you kinda have to either wipe out the other side completely and persecute all the remnants until the nth generation (see Russian Civil War) or you have to find some way to reconcile, even on a basic level.

That fact makes the victors very succeptable to guilt. Sometimes appropriately! Sometimes not. So.