I think people are much hardier due to Toady putting pack 40d style pulpings and they're not registering correctly or overstating the damage. I cleave someones neck asunder and their still kicking and don't even bleed out. In the past version that would have been fatal. Also, smashing someone in the head seems a lot less fatal even at higher combat levels. I'm not sure if this is intentional or not.
The "neck" is a new part, and I think it still has a few kinks to it. In previous versions, you had the throat, which currently is not appropriately related to the neck.
Though onto the main topic, if you kept auto attacking him, your character should've eventually pulped his head, I'm assuming your trying to do what you'd do in .34, and keep using aimed attacks to try to kill him. That still works in .40 just fine, but everybody is a bit more durable (in fact silver weapons are completely fucking useless now as a cutting weapon, used to be able to get by with silver in .34).
If you have a unconscious enemy, and can't sever him, just hold down a direction to auto-attack him until his sprite is a corpse.
So, yeah, while people aren't as fragile, the pulping thing lets everybody EVENTUALLY kill anybody else if they're persistent enough.