I've got threads on Ajokli somewhere around here and many posts. I believed him very important to the story, for many of the reason giving above. The Cnauir became Ajokli is nice thematically. Mimara saw the Prince of Hate, One of Ajokli's monikers. I just don't really believe it.
Matter of fact, I've thought this for sometime, I just can't square it within the text. When Ajokli is described, it's as a trickster, companion to the Gods, one that will lie to you, cheat and steal to get what he wants. He's known to give his Narindar's the power they need, only to take it all away when they need it most.
Doesn't sound like Cnauir to me. A man who is bound by honor and such. A great warrior who seeks vengeance. But Kellhus? Oh yes. Ajokli and Kellhus share many, many traits. Look at how he won the Three-Seas and became Aspect-Emperor. He lied, cheated and stole his way into power. Hell he murdered his own flesh and blood. If we look at what comes after determines what comes before, well, Ajokli and Kellhus kinda fusing together makes plenty of sense. I just can't square it, as I said through the text. If Ajokli just doesn't understand that Kellhus and him are one entity now would be the only way.