It is a very difficult one. Your GS was acting from pure instinct Lucky.
Prof Iain Hutchinson, an oral-maxillofacial surgeon who started the Facial Surgery Research Foundation and the charity Saving Faces which is linked to it, made a film about a woman with a severe facial disfigurement (which had resulted from an uncontrolled infection) walking down a London street and showed how no-one made eye contact, some looked away and even changed the direction in which they were walking. (the film went on to show how he operated on her and the improvement in her face after surgery).
I don't think you should ignore your GS's comment. I think you should explain that sometimes when babies are growing, things don't always work properly and that is why some children's faces look different, but the boy inside the face is just like him, and that is what matters. Also that the child would be hurt by his comment. At 4, he is old enough to understand that.
