"The issue at Peel raises questions about religious accommodation and how much influence a secular school board should have over prayer."

I disagree. The issue is how much influence a religion can have within a secular state school system. The answer should be none. The curriculum and timetable should be the same for all students. 

If different religions wish to set up a separate school system they should be free to do so, as long as they meet national standards of education, but they should not be supported by public money. The Catholic system unfortunately has been "Grandfathered" in, but there is no need to expand the separate system further, and I would have no issues with slowly phasing out this anomaly if it were politically possible.