Don't apologize for this essay its magnificent and you are so right.
I think the thing with the pardons for me, is that King Roald granted this pardon, and it was because he doesn't like fuss and trouble and Roger was a close relative, and it would be difficult and awkward and he didn't want to do such a difficult, awkward thing.
Whereas Jon grants this whole list of pardons and they're all for very specific reasons. He grants George a pardon because he has this very specific thing he needs from him, and then he grants a lot of pardons because he knows that if he starts his reign with a mass of executions he'll never live past it.
One of my favourite scenes in Squire (a long list) is the one where Raoul explains to Kel the difference between Warriors, Commanders and Heroes. And Heroes, in the Tortall books really exist to let commanders work. Like, when Nonsense goes down you need people like Alanna and Daine to defeat the evil sorcerer duke/defeat the nameless ones/distract the graveyard hag/yell at several gods. But by doing that, they make enough room for rule of law to take effect.
My favourite scene in Lioness Rampant is actually the council where Alanna is named champion, because she was already a hero when she left Corus in Hand of the Goddess... but there was all this controversy, and she was really unsettled, and she still wasn't comfortable with it (or her magic, or her gender, or her friends, or anything else) but she comes back a real established confident hero. And meanwhile, we haven't seen Raoul or Gary for a book and half and last time we saw Jon was his absolute lowest point. But Alanna walks back in as a hero, and she's greeted by these three fantastic Commander-Statesmen, who all fill in variations on the commander role, and are building rule of law, and are competent, and enthusiastic.
And Pierce is really sincere and serious about her world-building so there's no thinly veiled allegories, or snidness about the gods and immortals and etc. Its these three people (+ my beloved Duke Baird) who are trying to do exactly what you say, and instate this rule of law... but they live in a world of Gods and Monsters and Evil Sorcerers, so they need Alanna to give them the space to do it in.
And furthermore I also love (this is getting out of hand but its true), that after two superb hero characters (Alanna and Daine), we get Kel, who is a commander character... but she's much younger, so she has never known the randomness and feudalness that would have been familiar to Alanna, she's grown up under rule of law, she's used to Jon's overall level of success to the point that she can take it for granted and say "that's not good enough, we're not stopping here" which is superb.
And you're SO RIGHT about the historians.