There is a great deal of merit in the reaction and it does raise a number of important questions. First up, it is entirely correct that there was protection given to Catholic schools in Ontario (and Protestant schools in Quebec) at the time of Confederation. This has been described as a part of the original “compact” underpinning the establishment of Canada. Here is what Sir Charles Tupper said about this in the House of Commons:
. . I say it within the knowledge of all these gentlemen...that but for the consent to the proposal of the Hon. Sir Alexander Galt, who represented especially the Protestants of the great province of Quebec on that occasion, but for the assent of that conference to the proposal of Sir Alexander Galt, that in the Confederation Act should be embodied a clause which would protect the rights of minorities, whether Catholic or Protestant, in this country, there would have been no Confederation . . . . I say, therefore, it is important, it is significant that without this clause, without this guarantee for the rights of minorities being embodied in that new constitution, we should have been unable to obtain any confederation whatever. That is my reason for drawing attention to it at present.
An extensive discussion of this, including a confirmation that the existence of Catholic schools and the extension of rights to those schools is not discrimination under the Canadian Charter of Rights and Freedoms can be found in the Supreme Court of Canada's decision in Reference re Bill 30, An Act to Amend the Education Act (Ont.),  1 S.C.R. 1148.
It is also worth noting before wading into the waters of Constitutional amendment that the protection of Catholic schools has been the source of some of our most heated political debate, particularly around the abolition of Catholic schools in Manitoba in the 1890's. This was seen at the time as pure majoritarian attack on the rights of both a French and aboriginal (Metis) minority and does not stand as one of the prouder moments in our history.
However, as I have commented before, the existence of a publicly funded religious school system in Ontario does raise a number of public policy questions which do impact upon ensuring a strong sense of social cohesion in a society which now has many religious minorities. In 1867 the burning questions was how can we split Canada into two provinces (Ontario and Quebec) and ensure that the religious minority in each are not obliterated through the abolition of their school system? Remember to that this was happening the context of a world where in the not too distant past qualification for public office had been tied to being able to swear that one was a good Anglican and had nothing to do with the infamous Pope at Rome. The question today though is quite different -- we now live in a society where there are many religious minorities and it is inevitable (no matter what any Court says) that many of them will feel resentful and excluded when they see one religion getting a publicly funded school system while they do not.
Without trying to say what Ontario should do (that is a political question which requires a political debate) I think that the moral/legal questions raised at Ranting and Roaring can be answered as followed.
First, it should be noted what the protection given to Catholic schools by s. 93 of the 1867 Constitution was -- it was a protection from being cut back or reduced by the Provincial legislatures. There was no equivalent restriction placed upon the Federal government and, indeed, it was always seen that the Federal government could legislate with respect to the rights of Catholic and Protestant schools. The proposal to amend the Constitution thus takes away a quite limited procedural protection and it only does so with the consent of the Federal government (which was the procedural protection that was promised in the first place).
Second, the context of rights protection has dramatically changed in Canada since 1867. Now, because of the Charter of Rights and Freedoms there are actually positive substantive protections given to minorities, particularly religious minorities. These include (1) freedom of religion and conscience (s. 2); (2) the guarantee of the right to vote and to stand for election to the House of Commons and legislatures (s. 3) (thus no established religion); and protection from discrimination (s. 15). These restrictions apply both to the Federal government and the Provincial governments. It is worth noting in this regard that these rights as package have essentially given Catholics in Ontario (and Protestants in Quebec) far stronger protection from what they feared -- that is being forced to send their children to a Protestant school -- than s. 93. No government today could create a public school system that mandated religious education, much less religious education in a particular faith or creed.
Finally, David's point about aboriginal rights is without any real merit. The proper analogy to s. 93 (the section that protects Catholic schools) in the aboriginal context is s. 91(24). Section 91(24) is the provision in the 1867 Constitution that places the Federal government in charge of "Indians and lands reserved for the Indians". The theory again being that we would protect a local minority (the Indians) from a local majority (the settlers) by putting their affairs in the hands of a more distant, less directly interested government (the Federal government). Ironically in 1951 the Federal Government all but gutted this protection (except for treaty rights and reserves) by passing s. 87 (now 88) of the Indian Act which essentially said any Provincial laws that were unlawful because they interfered with the Federal power over Indians were made lawful as Federal laws. The complete abdication of the Federal role in protecting aboriginal rights is exactly one of the things that led to the passage of s. 35 of the modern Constitution.
Thus Catholics today (just as with aboriginal people) have stronger substantive protections of their rights than they ever had before. They are protected from being faced with qualifications on office or with forced protestant education. They are protected from discrimination. The question then is whether the social cost that comes in terms of dissent and a feeling of exclusion by other minorities is outwieghed by the social benefit of maintaining the Catholic schools. Answering this question is not simple and will require a real dialogue with the Catholics and others in Ontario. My choice, it I had one, would be to move on from an archaic system and reap the social benefits that come from a coherent secular public school system. This does not really answer the question of whether or not as a society Ontario should invest in this debate now.
My own feeling is that abolishing the Catholic schools system will not actually address the issue for many of the minority religions (who are largely driving the debate) in such a way that it is worth having the debate now. While the debate is framed in terms of discrimination -- why is it that the Catholics get while the Jews, muslims and others do not? -- that is not really the issue. The real issue I suspect is that many Jews, muslims and others object to having to send their children to a secular system which does not inculcate a core respect for religion and foster adherence to their parents' faith. It is for this reason that I expect many minority religion parents send their children to Catholic school -- even if the children are not educated in their parent's faith at least they are educated in a religious environment. Tearing down the Catholic school system will not change that and will not assuage the feelings of many minority religious parents.