As it stands the 3D models for kerbals seem to be hardcoded into the game as many mod developers have said.
This is a shame, and there's no real reason why it should be this way.
While Kerbals are adorable, and the current model certainly suit the game, there have been numerous mods to make the Kerbal universe more realistic in a lot of ways, but the stock animations and models are a constant reminder that the game isn't really all that realistic.
I personally like the universe around Kerbin unrealistic as it, but the mismatch between head shape and helmet shape has bothered me to an incredible extent since i first played the demo. So the fact that the suit and the kerbal heads can never be changed (at least not as easily as adding in new textures) is kindof a bother.
I'm also certain that it wouldn't be too drastic a change to make it possible for the game to use a different model, and make the bone and joint system of the kerbals available to modders.