It all depends on which era you are talking about.
There are mostly 3 different medieval eras; early, high, and late middle ages.
In Medieval Warfare: A History there is a chapter that talks about it. In the early and partly high middle ages, 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. In impoverished enviroments it was also better to take ransom, rather than lives. So battles were fought mostly on small scale, and casualties from the battle itself were few. 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-machine became more sophisticated, population increased, and the middle class arose and took part in non-equestrian battles using pikes and other less glorious but just as effective weapons. This led to large scale battles with more casualties on the ill equiped. So yes, as TomAu and fred2 said, there was a time when war took a great toll.
And this is especially true during the late middle ages and the introduction of gunpowder.