Could there not be a clause in the law that creates the Toronto regional government stating that the Province cannot disband or otherwise modify the borders of the new Toronto regional government without approval from the Region? Perhaps we could scale the 7/50 formula down to regional levels. This would require two thirds of the municipalities representing at least 50% of the Region's population to approve disbandment of the Region or modifying its borders.
Generally, no. The baseline understanding in our legal system is that the Legislature is supreme, and is free to change its mind. It can pass a law today saying one thing, and another tomorrow which says the opposite. Indeed, it can revoke early legislation either explicitly, or implicitly, i.e. to the extent that their is a conflict between the new and the old. In the latter case a court would say that the intention must have been to revoke the old, incompatible, law.
There are two ways around this problem. One is a Constitution, which is entrenched. The other are so-called quasi-constitutional laws like provincial human rights acts, etc. They're a bit more "sticky", and will tend to say things like "please interpret subsequent laws passed by the legislature in accordance with the following principles...", which makes it harder to argue that the legislature intended to undo its earlier work by mere implication. But at the end of the day they're just regular laws, and they can either be repealed by majority vote, or on a case-by-case basis by simply including a provision in a subsequent law to the effect that it operates notwithstanding the earlier quasi-constitutional statute.
I'm not at all familiar with these legalities, but I have a feeling that there's be some kind of framework to prevent this catch 22 I've described. A law dictating how itself can be modified seems like the kind of thing that we'd (usually) want to avoid. If this is true we'd probably have to go to the federal level to setup the formula for dissolving regional governments. Though that move would most likely violate the Constitution. I don't believe that the Constitution says anything about regional governments, however it does say that municipalities are under the control of the provinces. In a court case I doubt that the judges would allow the feds to control how regional governments are managed just because they aren't explicitly mentioned in the Constitution. It could successfully be argued that provincial control over municipalities implicitly extends to their control over regional governments.
Both the provinces and the federal government source their authority in the Constitution (see sections 91 & 92 of the Constitution Act, 1867). Don't think of it as a federal document in the sense of belonging to the Federal government. As I said, the powers are divided, and even if you could say that the matter of "regional" governments is within Ottawa's jurisdictions (perhaps by appealing to the pro-Feds catch-all provision, "POGG"), which I doubt given the explicit mention of municipalities, you'd still be at the Federal government's mercy.
Assuming that the catch 22 I described above won't work, we'd need a Constitutional change to prevent the province from meddling with the regional government.
Amendments that relate to local matters don't necessarily require the consent of other provinces under a 7/50 formula. I don't think that will realistically occur, but so long as this is framed as an Ontario-specific issue, rather than the creation of a new constitutional entity, then you may not necessarily have to canvas PEI's opinion on the matter. Also, there is the tricky issue of "Provincial Constitutions"--that is, Ontario's own constitution. In this province, like Britain, it's mostly unwritten, but some suggest that we could change that to allow some sort of entrenchment. Probably not giving the region a veto, but perhaps a document that had as one effect the creation of the region, a clause saying that general legislation touching on municipalities would not effect Toronto unless that is explicitly stated, and/or a clause that said the region could not be dissolved absent a 66% legislative supermajority. Again, it's *highly* speculative.
I have confidence that eventually these sorts of transit issues will be decided on a more regional basis. Someone earlier referred to lines drawn during Victoria's reign as dictating transit issues today. I'm not sure that's entirely correct. Toronto used to be much smaller, and it sat in a county that stretched all the way up to lake Simcoe. The importance of Steeles as a regional border only dates to 1953 when Metro was severed from York County, and at the time Metro contained 13 municipalities, not the 6 that amalgamated to form the present city of Toronto. Things change. As discussed ad nauseum there are models to choose from in other cities, and I don't think we should get too sidetracked debating the specific constitutional form such an arrangement should take.
). The whole point of that long ramble was about how the province strong-arms the municipalities too much. You know... "creature of the province" and what not. The city has no power over the province and obviously can't grant or take away power to/from the province. Only the province can do that. Maybe the federal government as well, but then we run into constitutional issues (ironically about the federal gov't encroaching on provincial jurisdiction). 
