Kellhus' original goal was to stop his father.

I'm not convinced of that. That may have been why the other Dunyain sent him, but I don't think Kellhus himself even made up his mind until well after he arrived in the Three Seas. Maybe even as late as partway through his meeting with Moenghus.

They engineered themselves this way with the Tekne, they have no excuses.

They engineered themselves so as better to pursue drives which were already dominant in their culture. I imagine that making pretty much everything sexual was a primitive trait for them, not a derived one. They may have made themselves even worse in the process, yes, but it's hard to imagine any slope being slippery enough for a human like species to modify themselves purposefully to enjoy raping infants to death on a species wide scale. Conversely, animals that have very poor fidelity in terms of choosing mates, and for whom mating is almost always rape, exist in the real world.

You assume that

1. Not having a mark means you are not damned

2. Aporetic sorcery leaves no mark.

3. The entirety of aporetic sorcery is just various ways to negate every other sorcery in the manner of the chorae

1 and 3 are unknown, and 2 is proven false multiple times in text. Chorae have a mark. A weird mark, a great emptiness. But it's a mark that an otherwise identical ball of iron that wasn't fashioned as a chorae would not have.

Have we considered the possibility that Maithanet was right, and Kellhus really was sparing his defective children for Esmenet's sake?

There is one scene in The Warrior Prophet where Kellhus has thoughts about Esmenet that are dangerously close to actual human affection. Or at least as close as a Dunyain can come to it.

During the First Apocalypse there were powers hostile to the Consult that didn't have to cross a continent of Sranc to assault the No-God. I think they were just being proactive in defending its existence.

I think I genuinely hated Esmi for a bit after that.

That was a painful scene, but I hated Kellhus for it, not Esmi. Esmenet had no chance against Kellhus.

If all sorcery is damned, would the Aporotic schoolmen be damned? Is restorying the world to the way it should be a damnable offense....

I doubt the Aporetic school was capable only of producing chorae. A school implies a whole host of teachings, not a single usable technique.

Perhaps they allowed Kellhus to come powerful first so they could murder him as a object lesson.