In doing so the Supreme Court turned the Charter on its head, running roughshod over the rights of a private institution. The Charter was intended to protect private actors (TWU) from an overbearing state (the law societies and the SCOC).
These two excellent columns discuss this decision at length:
Bruce Pardy: The Supreme Court's TWU ruling is a cruel joke played on all Canadians
Chris Selley: Supreme Court strikes a blow against religious freedom