I don't have any issue with a group being able to get a room in a public facility to carry out whatever they want as long as (a) the room was available, (b) the laws of the country are followed, and (c) the rules of school board are followed. The reality is that many things people believe in are based on tradition and things there is no solid evidence of. If people want to believe Americans didn't walk on the moon, fine. If people want to believe some guy magically made water turn to fermented grape juice, fine. If people want to believe an invisible and immeasurable being of which there is only one in the universe spoke to a guy, fine. As long as public money isn't paying for people to be taught religion and conspiracy theories in public schools I am good with that. Wear whatever you want, go nude if you like, believe whatever you want.
I find the need to split male and female washrooms outdated. How screwed up are we that we can't trust the other half of the population to share the same room when going to the washroom, but the other half the population it is completely OK even though you don't know them? I have to accept that I'm not going to convince most people that the idea of splitting washrooms by sex is an illogical way of thinking.
If someone goes into the cafeteria and isn't disruptive and gets kicked out because (a) they are a girl, (b) they are menstruating, or (c) not born into a specific population that is where I would have an issue because clearly the public school is meant to be public and should have the laws of the country applied to it and not the rules of a religion. However if that group wants to spell out who their target audience is without it being enforced I have no issue with it. If people want to have a Chinese Students Association then great, but if non-Chinese can't join then I have a problem with it. I only accept that religions can create rules which are discriminatory when those rules are applied inside a church, synagogue, mosque, etc because it is property owned by that group and like any private property the owning group can decide who comes on the property and who does not and the rules that are being applied on their private property are not new rules created in spite of current laws, they are rules that have existed before the current laws of non discrimination existed.
People believe in things that aren't logical and it is something we all need to accept. I will go buy a lottery ticket sometimes, but logically that is money very poorly spent. I admit that sometimes I am self-conscious with my appearance in a group of people who I don't know, don't need to know, and have nothing to gain by impressing and that also makes no sense. Human beings aren't fully evolved yet and some cling to beliefs from long ago. Many of those beliefs made a lot of sense in the time they were created and brought order and law to populations, protected people from eating meat that in times prior to refrigeration would have been more dangerous than other meats, made people less selfish in their actions (although with the threat of consequence maybe not so much in reality), etc. As long as we keep teaching people to think, action and reaction, math, science, etc and keep people with different beliefs alongside each other in peace I think our population will evolve to be more sensible and that is a good thing. I think having a large group of Canadians not grow up alongside other Canadians in harmony is a greater risk to our future than accepting that a group might believe in some things that others do not. It is only when a belief is put into action against the rights of those who do not share that belief that we need to be concerned and make sure measurable rights aren't being taken away from one group to solve an immeasurable negative impact to another group.