I would start with the dean of the department. If there is more hem-hawing around, go to VP of whatever (student services, education...they're different at every school.)
I just don't like the way this sounds, Bri. In this day and age where accomodations are made for all sorts of personal issues I find it hard to believe that he can just say you're affecting the class. He has issues with CA? Tough shit, fella...you're going to have to learn to deal with that.
As someone who works in higher education, I'm amazed that this happened. If he has any "real" grounds let him convince some of his higher-ups. Often I see professors who see themselves as infallible and godlike. We know this is not usually true! At the very least, he may have to examine his own issues and the role he is supposed to play.
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