The civilians don't die in my imagination, at least not much. Everyone gets troops immediately from conquered provinces, and it doesn't seem like people would line up at your recruitment centers had your troops been pillaging indiscriminately the day before.
I do, however, feel sorry for villagers in hotly-disputed territories: you never know, one day to the next, whose court system you'll be taking your case to (imagine having to start your case over, and over, and over again because the government keeps changing!). I also imagine that living in a heavily-fortified province must be annoying to the civilians (think the English before D-Day).