Which is my problem with the story. The stories shown are not about good vs evil. What passes for good in this story is a guy willing to brainwash or kill everyone in a country instead of saving them. This isn't a hero (except in classical sense maybe) or good and should not be treated as such.
They absolutely are about Good vs Evil. They're just not often about Right vs Wrong.
This is very much the point of the setting though, you have sides that (in the view of predominant culture) are
definitionally correct or incorrect. The guide serves as an exploration and rejection of the idea that morality can be
bestowed or commanded. The Heavens see all, and the Choirs are literally divinely correct, and a very major point is Anaraxes rejecting the idea that the Choir of Judgement's infallible foresight is even valid or relevant.
Even though said army still occupies near every position in the government and military, and the original leaders are denied a voice in government and later silenced(sure they were plotting a coup, but isn't that convenient for the author?). Yay for racial equality?
It's explicit that Amadeus has been slowly destroying Callow's capacity for self-governance for
decades. Catherine:
a) Utterly despises nobles
b) Is thin on the ground for options
c) Has personal loyalty as a noted character
flaw.
Catherine does actually want Callow to be self-governing, but most of the only people left don't have her personal trust and only have a self-serving interest in returning to form (because they believe their blood
entitles them to it). There are exceptions, people who actually put Callow first and despite Cat's loathing of nobility she bites back her dislike and gives them power.
Ultimately rebuilding Callow is going to take a long time.
They're also the unambiguous good guys and the story thinks its silly for anyone to think differently.
They really really aren't. Catherine finds the 'One Sin One Grace' ethos deeply fucked and a sign of Amadeus' madness. She has a personal attachment to them, and they're a vital tool, but they don't have a moral imperative because the legions don't have any morality or ideal beyond 'win the war'.
This doesn't fit with the earliest parts of the story when for example William had to live because of the Rule of Three or later when Cat/Black hinge their plans around their certainty of what stories are going to play out.
There's a wide gradient depending on how prominent or widespread the stories are. Roles and Names also make a major difference. Bumbling Conjuror is a name linked to providence far more than average, they're basically powered by ass-pulls, but if you just keep hitting them they'll stretch it too far and get killed. The previous Black Knight to Amadeus got killed by a random scrub because they ran into a group of soldiers and just got tired and overwhelmed.
Rule of three is a
very hefty story, and if it gets properly set up there's no real avoiding it (Except through things that aren't subject to narrative, like Demons). Although there's usually more than one 'allowable' resolution. Rule of three fight with a villain will end with the villain losing, but it could be death, or it could be redemption (followed by death. Redeemed villains almost always die in short order)
Yes, that's part of the problem. Good isn't allowed to actually be morally good (at least for the parts I've read), for Cat to be unambiguously good.
There are actually quite a few Good characters who are actually good, in varying ways. And Cat
definitely isn't unambiguously good. She goes through a
lot of development over the books, and later Cat regards a lot of her earlier decisions and beliefs with disgust. What Cat does is refuse to abrogate responsibility for her actions. She won't submit to an ideal and wipe her hands of agency. She and Amadeus have that in common, that that method of thinking repulses them.