With respect, your interpretation is just that--an interpretation. Doesn't mean it's the universal correct one or that mine's wrong. Emet-Selch is interesting for being a weird and ambiguous character.
The scene at the ladder, he actively works to remind himself that he needs to treat other people as less than him and other Amaurotines. He's also a character who builds himself consistently through inconsistencies. He talks about the scorn he feels toward mortals, but has spent more time trying to connect with them and mingling with them than any other Ascian that we know. He actively spends little time with the surviving Ascians, as confirmed by Elidibus. Emet-Selch tries to make insults about us (IIRC) clinging to lost causes, only for Y'shtola to point out he has spent god knows how long painstakingly making a fake Amaurot from his memories of somewhere dead and gone. He can't refute her there and just awkwardly admits she's right. This is an important precedent to establish.
Anger is easier than pain. It would be much simpler and less painful to claim that the genocides don't count because he's not killing real people, right? Way I see it Emet-Selch could work to convince himself of this for millenia, tell himself the counterarguments are stupid and moral relativism because seriously. What does it say about him if there's merit there? Gotta be dismissive and treat the very possibility like it's ridiculous.
Again. He said himself, he had children with mortals. Broke bread with them and died alongside them in an attempt to connect. He could have been doing things with the surviving Ascians. Frankly, I would have believed him more if he wound up closer to Elidibus' behavior-- "mercy kill" or "rescue these souls from an unnatural existence". Seek out the few unbroken Amaurotines who remain. The extreme reaction, specifically when it's paired with the weird hypocrisy and need to remind himself out loud and in front of the player, makes me think there's some doubt and tension going on.
Could you be right too? Sure, it's possible. This is fiction, part of the fun is finding a million ways to read a scene using the same evidence as well as possible. He could have just gotten sick of seeing ways that mortals aren't the same as Amaurotines and gotten frustrated by our attempts at survival.
Except there are quiet indications even in his own memories that suggest he knows he's not being totally honest with himself. We as outsiders can see the repression and desperate attempts to prevent any negativity from Emet-Selch's own memories in the shades of Amaurot. There would be no such hints at negativity even existing if he didn't know that same capacity existed even in his "perfect" city. And his whole process of needing to remind himself after being honestly moved by the display at the ladder literally shows us his process of convincing himself. That scene wouldn't be necessary and frankly, wouldn't have happened at all if what he felt was pure and honest disgust.
I felt bad about needing to kill him. It doesn't mean I don't see the need for it or that I would have done differently. It's possible to regret things came to that and wish it could have gone differently without believing you made the wrong choice under the circumstances. Ultimately Emet-Selch put the WoL in that position. And frankly, if he was realizing that his whole "they're inferior, they're not alive as much as Amaurotines" spiel was just lying to himself (another thing--he keeps moving the goalposts for that every time we meet his standards for being equals) it makes a lot of sense that he'd use us for death-by-cop. Either he wins, can continue telling himself that it's because we were less and unworthy and continue forward to bring the Amaurotines back... or he loses, is proven wrong, and the future rests with people who will survive as the equals of Amaurotines. His crimes won't continue, his memories will be put to rest, the burden of choice has been lifted and there is nothing he can do about it anymore.
To me, everything being literal and transparent for Emet-Selch makes less sense and is less interesting. Less tragic. I'm a fan of going in full-throttle with these types of scenarios rather than an answer that imo is simpler and more morally convenient. Because even if that doubt was there, if Emet-Selch is still trying to genocide all mortals then he still has to be stopped even if it kills him.
(Last bit, to clarify--there are plenty of characters who imo shouldn't have remorse or doubt or weird ambiguities because it would make less sense for them and limit what happens in human experience. Vauthry, imo it's important that we see he's extremely childlike in a lot of ways and truly believed he was doing something good. It doesn't mean we shouldn't have killed him, I mean the dude was basically doing forced cannibalism for heaven's sake. But it's important to really hammer home that he's not just evil for the sake of being evil because that's not how humans operate. Similar with Zenos, his motives for killing Varis, and his behavior throughout. He is literally crazy, there is something missing in how he thinks (empathy) that others have and it plays into every choice he makes. It would make less sense and not explain him adequately if he was just tragic. There are plenty of real serial killers like him. Saying he's only doing things for evil's sake and is a flat character misses a lot, what he does comes from apathy toward others and the purely selfish desire to not be bored/feel something and have purpose. If I thought something like that was going on with Emet-Selch or would be more effective, you have my word I'd be arguing that.)