No, it wasn't about getting religion completely out of schools, and yes, kids were forced to recite the christian prayer or conspicuously absent themselves.

The Mississauga situation is recognized, ordinary law of reasonable accommodations. Here's what an Alberta court said last year about a similar situation:

"Webber Academy characterizes the tribunal’s decision as a “precedent-setting decision with far reaching implications” With respect, that is not an accurate characterization. The tribunal applied well-established principles of law. For many years, public and private schools have been required to adhere to human rights legislation in offering their educational services to the public."