Call me what you will, but for me this is an incredibly fascinating area.
Jean de Paris, if you dont mind i may try to contact you via email or MSN messenger.

I have several ideas. The first is that you are right in that if there were civilians running all over during a seige, it would be too much, not to mention unrealistic. The only exception might be in a surprise attack, in which case theyd soon disappear to their homes anyway. The second is that it is realistic that a population decreases as a seige progresses, due to starvation, poor health etc. Also, when you destroy a certain bulding a number of civilians should die as well, depending on the building (barracks virtually none, homes many). The civilian death toll will have a negative affect on the soldiers, possibly causing them to desert (unit disbanding) after the battle.

If this doesnt work, then it may be possible to have peasant units (both male and female) in the city who cant attack, but you can still order them to move around like regular units. If the enemy soldiers kill the peasant units, they may disband after the battle, and if they kill too many they may even rout on the spot, the effects being worse for female units.

The exception to these would be fanatical units, perhaps waging a holy war or the faction's people were historically known to be fanatical in warfare in Medieval times (ie the Russians).
As a Japanese i know a thing or two about the positives and negatives of fanatacism in warfare. I have one more idea that i can share if this discussion gets hot, although if its going nowhere then thats fine too
-Pazu the Kitsune