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.
Do non haredi rabbis have a different Shulchan Aruch?
If there were no other option other than the Shabbos class, the fact that you need it for your degree wouldn’t make it muttar. Perhaps that’s true for the issur of hearing apikorsus as well?
Go ask a competent posek.