Well, I only attended one class so far, and I do not know if this clown will continue with his comments in the future. Really, his comments are not necessarily relevant to the teaching material.
Obviously, if the rabbi is haredi, he will say that it is assur to attend a class where the professor spews heresy out of his mouth.
But in this case I need this class for my degree, and the only other option [to take it with a different prof] is on Shabbos. Maybe I should communicate to the prof that his uncalled-for comments make me uncomfortable? But he is probably already aware of that.