It all depends on which era you are ralking about.
There are mostly 3 different medieval eras.
The early, the high and the late middle ages.
In Medieval Warfare: A History there is a chapter that talks about it. In the early middle ages and partly in the high, people were few and only the nobles and the clergy fought in wars.
Those two groups were pretty important and as time went on, heavily armored and well equiped. It was also better in impoverished enviroment to take ransom, rather than lives. So battles were fought mostly on small scale and the casualties were few from the battle itself. So the percentage according to the book (if I am not mistaken it was 5% exactly) was that low for the battle itself - excluding marching deaths, illness and other factors.
Later on though, during the high and late middle ages, the European war-machines became more sofisticated, the population increased and the middle class arose and took part in non-equestrian battles using pikes and other less glorious but as much effective weapons. This led to large scale battles with more casualties on the ill equiped. So yes as Tom Au and fred2 there was a time when the war took a great toll.
And this is especially true during the late middle ages and the introduction of the Gunpowder.