I think what's being overlooked is that the Baptist schools aren't actually being accused of violating anyone's Charter Rights. The Charter protects against discrimination based on sexual orientation, it doesn't command celebration of it.

What should disturb people, is the government is stepping on the freedoms of Association, and Religion. Freedom of association cuts both ways: you can choose to associate with something, or choose not to. Other people can choose to associate with you, or not. Someone may want to associate with the Baptists, and the Baptists may choose otherwise. Within very broad strokes, the government isn't supposed to have any say in religion. You can't kill someone, then try to hide behind religious freedoms, for example. If they can make the Baptists violate their religious beliefs, they can make the Muslims, and the Jews, and the Scientologists. Take note, Atheists, they could make you pray.