At the heart of the debate is the Education Act, which forbids religious exercises in public schools, versus the Charter of Rights, which guarantees religious freedom.
In such a multicultural country as Canada, and particularly in communities where large numbers of ethnic groups have gathered, I think the protest is unfounded. While some take the stance that because we are so diverse we should take all religion out of schools, I advocate for embracing them all instead.
Something like the Education Act is a general or national law that completely ignores the needs of smaller communities, and by that I simply mean local needs. The Toronto School Board has been experimenting with a race-based school, specifically for African Americans. They heard the members of their community talking about the need for students to learn more about themselves and their history, acknowledging their background rather than trying to ignore the differences between cultures. The school mentioned in the article above also saw a need: 1/4 of their students were leaving the school every Friday to walk to the nearby Mosque. Some students never made it to the mosque, many never returned to school afterward. To preserve class attendance, and, more importantly, to ensure student safety, the prayer session was allowed into the school. I see it as a triumph, a way for community members to gather, a way to open up dialogue between religions and races.
For the groups that are protesting (Jewish, Hindu and Christian), I wonder why they might not counter with having a group of their own. I think of the religious class in my own church, called Seminary, where high school students attend a bible study class every morning before school starts. While it currently takes place in our church, because it is right next to the high school, in another city it might be easier to have the class happening right in the high school. I would much rather see school officials and parents work together to increase awareness and understanding of cultural and religious differences than to hide them away from others, which would only feed ignorance.
I concur that there must be an "all or nothing" attitude when it comes to this issue, but I see many more benefits to the "all" approach than the "nothing."