The difference is : A church is protected under religous freedom, but a public tax payers institute, (such as a school), isn't.
They should not be teachings things are wrong if they are totally legal under government laws.
Such as abortion, gay marriages, or even common law relationships.
I can hear Morelucks outcry if it was an Islamic School, being public funded, teaching their female students, that it is wrong not to obey pre-arranged marriages, or wrong to not obeying their husband, wrong to cast a vote, or wrong to drive a car.
Even though, that religion has been around longer than USA and Canada together existed !
The public funded schools should not have the right to teach against our freedom of individual rights of our country, period !