'Ends justifies the means' ethics are still motivated by will.
That's not something i would contest, every action a living being performs is the result of a will and a purpose.
So the question should be diverted from debate about whether Kellhus' methods fall outside normative morality to what his real goal is.
If he is really acting to save humanity from extinction, then his will is good - whatever the consequences of his methods.
I did contest the objective definition of goodness though. If you agree that extinction (or something close to that) is the single worst thing that can happen and if you also agree that Kellhus' path is the only path, you will see him as good. I believe neither of these things, so i have a different opinion on goodness.
Even if i changed my mind about extinction due to it's finality, i would still not accept Kellhus's opinion that his is the only path. If i judged his actions according to his own opinions i could do the same with Hitler and dim him good, as long as he sincerely believed he was advancing humanity.
I think you should consider the part of history as the causal darkness of much of the horror and suffering in Earwa. I don't see how the New Empire is much worse or better than the way things were under the Kian/Nansur/Thousand temples et al. Changing the history of stagnant, dwindling civilizations (secretly being guided by genocidal monsters towards extinction) doesn't seem like a bad thing to me.
There are huge differences in my eyes though. If Kellhus is indeed laboring for the good of mankind he should have gotten rid of most of the old system. Instead, not only does he make use of most of the old system to better control the population, he establishes a theocracy. So his tyranny isn't just of the body, it's also of the mind. His subjects can't question his actions, they can't even feel dissatisfied because unlike his predecessors, Kellhus is God.
What Kellhus does is to sacrifice freedom in order to increase security. I am with Benjamin on this one. Besides, if Seswatha could unite mankind against the Consult by telling the truth, i don't see how a Dunyain couldn't do the same.
And I must disagree with your statement about Alexander. That is just so incorrect to me. He destroyed the most stable and effective imperial structure in the ancient world and left internecine chaos in his wake that destabilized civilization in Europe and the near east for hundreds of years.
What you state isn't antithetical to what i was saying. Alexander was a pupil of Aristotle, thus he believed great actions make a man immortal. He made war to the known world to feed his narcissism. Nations were enslaved, countless lives were lost, and in the end when he died his empire fell apart. But most people pay little attention to those facts. Instead they give weight to the fact that he managed to conquer all the known world. This was something that no one thought possible before Alexander, but he showed the world that this possibility existed. Do you doubt that Alexander, to this day, is admired for his accomplishments by the majority?
Also, Dunyain have the ability to empathize beyond comprehension. What they lack is sympathy.
I was talking about empathy as an instinct. Dunyain observe their subject's face and deduct it's intent according to what they know of it's history and beliefs. Empathy is an instinctive reaction to people, and it uses the self as a comparison, that's why it produces sympathy. For example when Kellhus feels outrage for Serwe's abuse he empathizes instinctively with her. Empathy isn't active, it's passive, Kellhus doesn't want to put himself in her place, it just happens.