> Since critical thinking is performed by humans, surely the same human ‘flaws’ apply.

Oh absolutely. And that's just accounting for actual critical thinking in which human flaws enter the equation and muck things up. Huge swathes of public intellectuals claim to be rational, objective, critical thinkers all the time when they're spouting complete nonsense, usually for a paycheck.

> I would think that having characteristics of humanity is not necessarily bad for a human oriented system, and I can also point to any number of atrocities that were the ‘perfectly rational’ course of action for a statesman, nation or movement at some point in time.

I would also add to that, that a purely rational worldview or thought isn't even necessarily a good thing. We will never escape the foibles of our human limitations (at least, probably) but in the same way, we must always retain our humanity too.