In the context you raise, the notion of "freedom from religion" is misleading. It trivializes the actual freedom in play, which is freedom of belief. 

Canadian citizens may believe, or disbelieve, anything they wish. I'm not aware of a single instance, ever, of an adult Canadian being forced into believing something against their will. Certainly that's not happening at TWU. Students are free to believe whatever they want. However they VOLUNTARILY agree to follow certain rules, which is a different matter altogether.

It's generally true that you may not have your rights materially impacted by others. And the courts have already noted that TWU doesn't materially impact the rights of LGBTQ students. LGBTQ students have many other options for an education. So there is no material infringement on their rights.