The problem with whips is that DF doesn't consider any kind of weapon to be made of multiple pieces; to DF it's all one rigid body. The tip of the whip hits with high speed and small contact area (as it should) but with the full weight of the weapon behind that blow, not just the weight of the tip. It's not really a lightsaber, it's a bullet - well, a short range bullet, but same effect when it hits. High speed, ridiculously high weight (results in bullet-like force), small contact area, goes clean through metal and flesh and fractures the bone beneath.
It's an easy fix - go into the raws item_weapon file and reduce the 'size' of whips and scourges by about a hundredfold. The result feels more realistic to me: they're poor weapons for actual warfare, almost always deflecting off decent armor, but are still dangerous to unarmored dwarves. And like any weapon, there's always a small chance to get lucky even against a fully armored dwarf and hit him somewhere vulnerable. If you're going less for 'realism' and more for 'balance', i.e. you want whips/scourges to be not so overpowered but at least on par with other weapons on the battlefield, reducing size by somewhere around 1/20 should do it*.
*Disclaimer: I have used the 1/100 reduction extensively but not the 1/20 one, it is a rough estimate, I take no responsibility for any gunshot whip wounds your dwarves may suffer.