The larger an organization grows, the more complex and arcane and bureaucratic it gets. More and more weird emergent behavior pops up that isn't directly related to the original charter of the organization. Companies, governments, academic institutions... all across the board.

Is it any surprise the code we right at the direction of these organizations does the same thing?

In other words, I don't think it's our relationship with code turning us into automatons. I think its our relationship with each other that pushes both our organizations and our code into those paths.