Yeah, but I think Kellhus being a heartless dick about people's suffering is sort of par for the course - he's being Dunyain. I think he knows that anyone, male or female, would have been vulnerable to the Inchoroi (and would have enjoyed that vulnerability - and yes, it is incredibly creepy and disturbing), but he's analyzing why Esmenet in particular is ashamed of what happened. Namely because of her own history as a whore. And from there he looks at the reason that history exists.
It's not like Cnaiur doesn't suffer similarly bizarre sexual...assault?
It's a given that Kellhus regards everyone as a tool and little else - and while any character in the book suffers and a score of them get thwarted permanently, i.e. fatally... none of them are as outright pathetic as the women in these books, which is really a shame, considering how much promise Esmenet's character showed in the first book. - Let's better not mention Serwe, ugh.
Cnaiur on the other hand was specifically the only character who, for the majority of the books, could see through even the Dunyain's tricks and tried to follow his own agenda. Ultimately he was twarthed, as all of the Duneyain enemies - of course. Still, that's a huge difference to Esmenet who appears to sort of lose her own will permanently at some point and ends up being the playball of whoever is there at the moment, be it Achamian, Kellhus or some Demons (Sarcellus early on even foreshadowed this development, i guess.)
Aside from the misogyny I am also somewhat disgusted by how the trilogy starts out with immensely interesting multidimensianal characters that become less and less interesting the more contact with Kellhus they have. I understand that this is part of the point Bakker wants to make: Kellhus rewrites their souls, the old characters are de facto dead, the new guys get modelled after whatever Kellhus needs, which basically goes hand in hand with Nietsches view on Nihilism and the Übermensch... but what it means is that it quickly becomes an ordeal to work through page after page that is written from these "rewritten" (now by Bakker) characters point of views, which brings us back to Esmenet, where that issue is most pronounced. I wouldn't even be surprised anymore if Bakker turned her into a "Serwe" at some point. The transformation would then be complete.
Ironically i find that without the Duneyain and especially without Kellhus, we might have had the basis for a much more interesting story. I would have loved to see these intriguing characters from the first book evolve... instead of stagnate. Although, I have only read the first trilogy at this point, so I can't speak about further character development in the next books.