Now of course i could be wrong and Kellhus is blind to her (as he says) and motherly love might be beyond his knowledge, and i'm inventing this narrative.
I don't think he claims to be blind to her, just to his own motivation when it comes to her. But I think he couldn't have predicted she would act the way she did. When he "armed" her against Inrilatas, he also armed her against himself. Like Moe sr. made Cnair hard to predict and control, Kellhus himself made her hard to predict and control. I don't think it's so much motherly love as being able to see through Dunyain manipulation making her actions unpredictable. But she has conflicting emotions about her kids probably also complicates things.
In TPON, Kellhus reveals some of the Dunyain weaknesses when dealing with mortal souls. They do not assume they are dealing with rational actors; rather, they assume they are dealing with creatures that respond to stimulus that can be understood by those with the Dunyain gifts, while remaining unknown to the people themselves. In this way, the Dunyain can dominate them utterly and use them as tools.
Cnair is somewhat more difficult for Kellhus to control, and even surprises him at times, simply because his actions have become unfathomable. His detachment from reality means his actions no longer reliably follow the principles of the logos.
By the same token, I figured this was the reason Anasurimbor Serwe was not able to dominate circumstances at Ishterebinth. I mean, if anyone could rally the intact and bring the erratics to heel, it would be a Dunyain. She could have pulled the Tall from the Mere, and shown up at Golgotterath with a pretty fearsome army. But Kellhus would have known that their insanity could not be mastered, and Serwe learned during her, uh, time as a guest of the Nonmen that it was a lost cause and they had completely fallen from grace.
Of course, by that same token, I don't have any explanation why the nonmen showed up during the assault on Golgotterath. If they were hungry for glory and destruction, Serwe would have known and so controlled the circumstances, rather than the clusterfuck that happened once senile Quya found themselves on a battlefield with not one, but two different ancient enemies.