Cover some of those things taken to their extreme and require that a character be evil to take them. A character with one of the physical or mental features granted by a deformity feat, that doesn't have the feat is still perfectly RAW legal. He just gets no benefit or drawback from being deformed. Or are you actually arguing that deformities should be beneficial to everyone that has them?
For example, there was an entire thread on obese characters in D&D in the 3.5 subforum recently.
Edit: upon further review only self mutilation and obesity are covered by the deformity feats.