Alright, follow some procrastination, experimentation and some test subjects dying from old age, this is where I arrived at:
I have made all face-bits internal safe for the eyes, reduced their size and removed lips and cheeks on creatures that use the 'FACIAL_FEATURES' bodypart entry, which is about all humanoid creatures at least. Somehow this does not actually seem to result in noticeable errors with the descriptions.
Its not perfect, as things like ears but also the tongue and mouth behave like internal organs, but all other solutions either require me to alter just about every creature entry in the game, or just plain don't work. Embedding them should work the same way it works for fingers and throats, but its bugged for helmets. Bodypart relations like the ones skulls use don't work reliably either. There is also no way to transfer damage to an embedded part to the parent bodypart. I tried removing all the completely superfluous bodyparts by just leaving their raw entry empty, but that generates a flood of errors.
The AI can at least no longer target lips and teeth and such, though it comes at the cost of silly combat reports like blows glancing off the helmet, doing no damage, yet still somehow tearing apart an ears, noses and... tongues. Which is also the reason I left eyes as they are. That and hitting eyes through a helmet actually makes sense. Teeth can still be damaged but stopped flying all over the place, kind of a shame but at least it doesn't render all your soldiers toothless after a while.
Replace the contents of body_default with this:
http://pastebin.com/7ivj3nRt to give this a try, it will be released with the main mod after I'm done making vain attempts at a more graceful solution.
Also making ears into joints causes the AI to get stuck endlessly bending someone's ear, which is kind of funny.
The scratch attack does seem more glaringly silly now. It would be fairly trivial to remove on the entity and beast races...
Other stuff I have been working on is mostly minor weapon balance/bug corrections as well as slews of item descriptions. Looking forward to any feedback you may have!