I haven't spent a lot of time on this, but I thought Kayûtas and the state of his mental faculties during the Meat episode was very ambigious. It is established fairly early that although they are seen as holy due to their relationship to the Holy Aspect-Emperor, generals and menials alike are unnerved, even frightened of Kellhus's children. Kayûtas is a foil to this; Proyas (or so I read him, at least) thinks of Kayûtas as the reasonable son, the boy in the family that seems most human, without losing any of the sharpness of mind and sight that characterizes Dûnyain. My first interpretation was that Kellhus left Kayûtas behind knowing exactly what the Meat would do to the Men of the Ordeal, and instructed him to partake in the acts of madness, all as a part of fooling Proyas into giving the command. If Kayûtas himself, Kellhus's son, succumbs to the madness, then Proyas has only one choice. It becomes clear as day that the madness is all-reaching. If not even the Lord-and-Prophet's blood is safe, then certainly that would give implicit support to his decision to sanction cannibalism. The madness takes all, as it were.
Maybe this is taking it a step too far, and the Meat episode really just showed how far removed Kellhus is from his more worldly children, but I thought it would have been devilishly clever to have Kayûtas indulge in the very depravity Kellhus knew that Proyas would struggle with. Now, if that really was the origin of Kayûtas seemingly mad episode, then that makes him an all the more convincing and terrifying character, because it shows that he is able to set aside sentiment to serve the aims of TTT.
