Separation of Church and State is a good thing. That has been demonstrated numerous times. The moment you give any religious group funds or recognition, then the govco is tempted to begin controlling religion. Religion is a natural tool for government to use, and the govco naturally then begins to use religion to control people and combines with the religion to create something unique. Its demonstrable in History. So Sharia cases should not be adjudicated by Canada's supreme court and technically are not and neither should Halacha. The cases in the article are civil, not criminal.
Here is the thing, however. When a visiting power (whether Jewish or Muslim or Christian or Other) presses for political influence, it should not be recognized as legitimate. These are visiting powers which are religions and which operate under the protection of the government in power but not above it. So if there is a dispute in a religious court which affects a citizen of Canada, then jurisdiction must reside with the courts of the law of the land. Generally they do.
Here is what is different however. Today we have evidence that fundamentalists do not respect the law of the land. Instead they insist that the law of the land should be subjugated to the laws of their particular religions. This is not OK. A legitimate fear is not the actions of a few but of the idea that the natural government may be subdued by activists claiming religious authority. It is a real threat to government by the people and has occurred in the past.