The simple answer to that suggestion from a 'senior' Apple tech was 'No, we will not replace the machine. Wait until the logic board is replaced'
Where is the repair being done? Locally (e.g., at one of the Apple Stores in Toronto), at the Flextronics factory in Austin, or in some other manufacturer's repair center?
If it's being performed by Flextronics, I'll offer a contrarian option: as long as Apple agrees to reinitialize your warranty term, you might wind up with a better computer after the repair than you would with a new one. When a manufacturer's service facility repairs a product, it often is subjected to pre-shipping tests that are more rigorous than the standard factory QA process.
I certainly was pleased with how well Nikon-USA repaired my D800E, which exhibited the infamous left-focus problem. I wasn't at all happy with how long it took the company to figure out how to perform the repair—several European and Asian Nikon repair centers reportedly were dealing competently with the left-focus problem months earlier—but at the suggestion of Thom Hogan I waited until Nikon-USA got its act together and, when I got the camera back, not only was the left-focus problem resolved but the phase-detect autofocus was generally improved no matter which focus points were used. Similarly, I've been delighted with the two factory-refurbished Nikon lenses I purchased, while on at least one occasion I had to send a bad sample of a new lens back to the retail seller.
I agree that Apple ought to honor your request for a replacement, given that you only had the product two months. But if I were in your position, I think I would at least wonder whether that was the best approach.
One other thought: I've been very pleased with my Mac Pro (so far
. . . ), but unless your experience was the result of a unique combination of simultaneous problems, it strikes me that what happened may reflect an engineering failure. A computer that crams so many components into such a small form-factor needs to have a really foolproof thermal shutdown mechanism. If a fan problem precipitated the meltdown of your motherboard, that raises questions about the robustness of the design. (Guess it's time for me to pop for that "Applecare" post-warranty maintenance contract.)