I'm trying to remember, but I'm not sure he fully gets the banality of evil.
From my fuzzy recollection all the antagonists in HDM weren't very three-dimensional. It was all faceless bureaucracies, authoritarian religions, nasty people pretending to be nice, and "end justifies the means". It was all bad people doing things everyone knew was bad, so they hid it, but they justified it. Not people thinking they were doing good, and doing so publicly and being cheered on for it.
I don't think he could have invented something like Mermaids, although they could have existed quite happily in Lyra's world, maybe a couple of decades after the first experiments in Northern Lights. Susie Green would fit in perfectly, extolling the virtues of the procedure her child underwent.
Regardless, whether a writer "gets it" or not, there's a huge difference between writing about being a hero or standing up to authority and actually doing it.
How can you reasonably expect a writer to be able to do such things any more than you'd expect them to do any other things their characters might do? (Same for actors.)
Knowing how to do something or even just knowing that something is done is not the same as being able to do it, or even wanting to do it. (Good or bad). Their skills are writing or acting - that doesn't directly translate to any other real life skill they might portray.