WillSea - if free will 'exists' in any sense, it's unlikely that rational choice theory or its wider adoption could push our "chance to exercise it...out the window forever." Perhaps Bueno de Mesquita's predictions have a 97% level of accuracy because it would be generous to grant that people exercise (or have ever exercised) free will 3% of the time, in cases of "gamesmanship" or otherwise. Even Kant, champion of the autonomy of the will, would have conceded something like this.

So I agree that we should approach this 'tool' with caution--a political science bereft of regulative ethical principles might have trouble coherently justifying even its own 'objectivity'--but I'm not sure to what extent free will, if it's not an empirical matter, and if it doesn't seem to be exercised very often anyway (at least not by the criminals, mobs, or political actors most commonly analyzed in game theory), faces a new or newly apocalyptic threat here.