The way I look at the matter is according to rights afforded by the Charter. In this case the competing principles are freedom of religion and association, versus equality rights. I then look at how the Supreme Court has adjudicated cases of competing rights in the past. Who the antagonists are isn't of any personal interest to me. I'm a heterosexual atheist. I have no axe to grind in the case, other than seeing that justice is done according to the Charter and to the legal framework that applies in such cases.

"The problem is that TWU's covenant discriminates against LGBT students in particular, and anybody who doesn't adhere to evangelical religious views in general."

Again, you really should read the covenant before making claims about it. The restriction on having sex outside of a man-woman marriage applies to everyone, regardless of their sexual orientation. Far more heterosexuals are affected by the covenant that non-heterosexuals.