But this misunderstands incentive based analysis.
The point isn't just that people naturally follow incentives, but that those who refuse are punished and no longer in a position to affect the world.
Taking a principled stand is great and all, but if the result is simply that you get fired and replaced by someone better at following orders, you didn't really fix the problem.
Of course it's more complicated than that. Certainly other people being willing to do evil is no excuse to do evil yourself. Maybe your principled stand inspires others and you start a revolution or something. But that's rare. In the average case incentives win. Which is why if you want to actually change the world for the better you should attack the incentives not the individuals - individuals can be replaced, but millions are willing to follow incentives.
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The rest of the article seems to be about developing your own morality, but morality is really just yet another incentive.