It's kind of impossible to have empathy for someone who doesn't have empathy. Once you try to put yourself in their shoes, that's you being empathetic and, as such, failing to put yourself in their shoes. It's like trying to "win" The Game, the act of trying to win causes you to lose.
Shunning, however, is absolutely an empathetic act when done to someone who society has deemed incompatible (which is very few people all told, most just need a hug), especially when considering all the other varied and violent methods humankind has developed for dealing with these sorts of issues over the millenia. Not only is shunning vastly more empathetic than torture, rape, dismemberment, etc., it's also more empathetic to society as a whole to have that person removed.