Its hard to prove without the counterfactual one way or the other.
Crystal Dynamics and Phil were clear that Microsoft helped significantly with development, resulting in the game being excellent. After costs got so out of hand on the first game, its likely that that assistance was integral to the game being so good.
Given the game would have been of poorer quality without the exclusivity deal, I think its clear that in the long run, the deal was healthy for the franchise - at least for those who are interested in it.
From a purely sales perspective, its even harder to speculate. Had the game come out and got a Metacritic of say, 75, due to it being poorer for the lack of investment from Microsoft, this iteration would have suffered heavily. That, in turn, would have effected perceptions (and investment) for the third game.
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