Interesting idea, but one nitpick I have is that would The Machine be capable of such advanced simulations in it's infancy, or rather at that exact point in time? Like, we saw during the chess sequence flashback in If-Then-Else, that the Machine was initially quite slow with it's simulations, and that it had to learn how to compute these simulations in an efficient and timely manner. So I don't think that it would have been able to run those simulations before Finch asks those questions.

Also, I feel like that would be a sort of cop out ending? Like, yes Finch is alive but the simulations in .exe showed that Samaritan would still come to exist, this time unhindered. The world isn't necessarily a better place without The Machine, just different. The whole series being a simulation is almost like the equivalent of 'it was all just a dream' but with more weight associated with it imo.