If Ontario boards are legally required to provide religious accommodation when it is requested, then it is time to change the law.  Our state run schools are no place for partisan religious practices that inevitably lead to arguments of the type outlined in the article.
Separation of church and state is one of the fundamental tenets of our way of life, and despite the historic importance of religious accommodation in developing a tolerant society, we need to recognize when religious accommodation brings more trouble than benefit to our state run enterprises, and threatens that fundamental tenet.
Religion is religion.  Politics is politics.  Allowing those ideas to get mixed up has produced enough strife and conflict in this world.  We need to evolve to take the lesson from that sad experience and move forward.