The article says:

Children report having to hide to pray at school, says head of NCCM

[…] students have been threatened with disciplinary measures for praying at school. […] a student who was mocked by a teacher for trying to find a place to pray.

[… Education Minister] said students would still be allowed to pray silently and discreetly. But […] that’s not an option for Muslims, whose prayers require physical action.

The case was brought on behalf of a 16-year-old Muslim student at a Montreal-area high school who had been given a place to pray during the lunch hour but lost that accommodation after the ban went into effect. […] Sworn statements have also been entered into evidence from three other Muslim students who say they also lost the ability to pray.

So in fact, it’s not that the law doesn’t allow schools to set up multifaith chapels, the law doesn’t even allow the principal to say “fine, use that closet for 10 minutes a day”.

And even though the minister had said people would be allowed to pray “silently and discretely” they have not been allowed to do so.

RE: “cool kids hiding”: they are reporting that some kids are hiding. In the eyes of their peers, this can become, over time, a badge of in-group coolness. If you don’t understand that, you haven’t been around religious teenagers. And yes, you can avoid giving religious extremists clout, by not making them into symbols and martyrs. You want their moderate peers to feel comfy enough to turn to them and say “take it easy bro, things are nowhere near as bad as you describe them”.

Look buddy, I’m a secular atheist. In this case, ultimately the law is just being dickish. Schools don’t have to officially support prayer, just tolerate it. Superstition is not going to be wished away. But if you keep a lid on it and don’t feed it with outrage, it just withers away.