If you want to refer to somebody who knows what he's talking about, and defends the contemporary court, there is Jake Ziegel in today's Globe. Ziegel is a leading expert on court appointments and compensation, and he knows that the Provincial court judge's reference created a mess. Ziegel likes the Secession reference, which is his right, but we have yet to actually experience what it will mean in the event of a secession vote.
Almost everything else the Pithlord has read in the national media is crap. In particular, it trades on confusion to pretend that the Supreme Court of Canada has not engaged in a revolutionary overthrow of our constitutional order.
The first confusion is between the existence of unwritten principles as canons of interpretation and controls on executive government and unwritten principles as the basis for declaring legislation invalid. The former have always been part of our system, and are probably inevitable in any legal order with limited government. The latter is a new innovation dating back to 1997.
A more subtle confusion is between the institutional question of who has the final word -- the court or the legislature -- and the methodological question of natural vs. positive law. Natural law holds that there are some underlying principles in any just legal order which are accessible to all normally-constituted people. I agree with that claim, although I don't feel like justifying it here.
I doubt that natural law will tell us much about judicial compensation, tax policy on legal bills or the proper formula for a secession of a province, but who knows.
But the question of natural law is orthogonal to the question of the proper institution to have the last word. Whatever institution has the last word, it can be said to be bound by natural law (and by accumulated customary right), but it can only be bound internally. Since that institution has the last word, if you think it has ignored natural law, there is no one you can appeal to.
This is equally true whether the institution in question is Parliament or the Supreme Court. If the Supreme Court has done something fundamentally immoral (e.g., the Dredd Scott decision), then, since it is final, there is no human authority that can overturn it. On the other hand, if there is a system of legislative supremacy (with an override clause, for example), then if the Supreme Court violates natural law, it is still possible to go to Parliament to overturn that decision,
The same applies if Parliament has the last word. You can still say that Parliament has an obligation to be bound by natural law, but the obligation must be internalized by Parliament itself.
The difference (in addition to the principle of popular election) is that Parliament's word is never really final. It can always be opposed at the next election. Courts, by their nature, claim to state the law for all time. I have no particular objection to this in a system of legislative supremacy, but it does amount to "god-like power" in a system of judicial supremacy.
Finally, there is confusion as to whether the principle enunciated by the Chief is really a new one. I have tried to collect a few more citations of the principle of legislative supremacy in Canadian law, since, in the long run, it will inevitably be Google who determines this issue. As most lawyers know, there really are thousands of such statements by the courts prior to 1997:
The Courts of law cannot sit in judgment on the Legislature, but must obey and give effect to its determination.
Labrador Co. v. The Queen,  A.C. 104 (P.C.) at p. 123
The mistiness of view as to possible grounds on which an Act of Parliament might be avoided by the Courts has been cleared away by the modern doctrine as to the Sovereign power resident in the Legislature, and I do not know of any example, even in early days, when a concrete case arose of an Act of Parliament being overruled or displaced by the Judges.
Smith v. London (1909), 20 O.L.R. 133.
It is often said that it would be unconstitutional for the United Kingdom Parliament to do certain things, meaning that the moral, political and other reasons against doing them are so strong that most people would regard it as highly improper if Parliament did these things. But that does not mean that it is beyond the power of Parliament to do these things. If Parliament chose to do them the courts could not hold the Act of Parliament invalid.
Madzimbamuto v. Lardner-Burke and George (1969) 1 AC 645. Cited by the SCC in the 1981 Patriation Reference.
It would be anomalous indeed, overshadowing the anomaly of a constitution which contains no provision for its amendment, for this Court to say retroactively that in law we have had an amending formula all along, even if we had not hitherto known it.
1981 Patriation Reference (This is a cool bit of dramatic foreshadowing, since the court said exactly that seventeen years later in the Secession Reference, in regard to a formula for provincial secession.)
It has become a truism that the totality of effective legislative power is conferred by the Act of 1867, subject always to the express or necessarily implied limitations of the Act itself.
Murphy v. CPR, (1958) SCR 626 at p. 643.
The rule of law requires judges to uphold unwritten constitutional norms, even in the face of clearly enacted laws.
Chief Justice of Canada Beverly McLachlin, December 2005