One idea I've had is to make a glove that basically consists of a missing finger "plug". That way, I could simply force the glove to be equipped after the finger has been taken. Unfortunately, I'm not sure whether or not equipment can be flagged as "unplayable" in Fallout 3, so this method would probably have drawbacks of its own, but it's definitely preferable to destroying the arm entirely.
I assume the same method could be used for removing the ear. Although it would cause any glasses/gloves etc. to be removed, I suppose you'd remove them anyway before you took their ear/finger, so it makes sense.
Cipscis