I feel like somewhere along the line the writers forgot that the angels are all supposed to be siblings. They're an example of an extremely dysfunctional and toxic family filled with petty infighting. The Cas/Hannah thing and the Jo/Lucifer thing become extremely uncomfortable when viewed from that perspective. Angels aren't supposed to desire intimate relationships at all, but they especially aren't supposed to want them with each other.
Naomi confirming that Cas had been defective from the start was one of my favorite additions to his character post-Kripke. I felt a little conflicted about the whole angel programming thing, because hard-rule lore invariably results in retcons and inconsistencies and I think it was cooler and more magical when the lore was more abstract (heaven was so much more interesting in Dark Side of the Moon than as a white hallway and a couple of corporate conference rooms). But the angel/robot analogy seemed in the spirit of what the angels were always supposed to be. And Naomi's "I think you came off the line with a crack in your chassis" is so iconic for Castiel.
Given that, I think the direction they went with for Apocalypse World Castiel was disappointing, silly accent aside. If Cas really was predisposed to disobedience then I like to think he would have objected to Micheal's reign and the genocide of humans even without Dean's influence. In that scenario I assume Michael would have just killed him. But they wanted a cameo, so they went with ruthless torture nazi. It's defamation, I tell you.
Kind of a side bar, but I love the fact that Misha initially chose to play Cas as cold and emotionless because he wanted demonstrate how alien the angels were, but then none of the other actors playing angels followed suite, so it made that behavior less of an angel thing and more of a Cas thing. He's just a little bit special, is all. Maybe it's from all the times Naomi has fucking around in his head.