Genocide of any seems far from a justifiable action that would allow El'Duran to pass through Maltheal.
I guess it comes back to the question of does the ends justify the means...
How does Eldruin justify something as righteous anyway? Does it have a moral standard? If it is it's probably a standard that goes beyond mortal understanding and/or normal convention. Maybe it's a standard biased towards the High Heavens but who knows.
That same question can be asked for Kal-El killing Zod, or Batman refusing to save Ras.
Also.. if Maltheal aim in RoS is to kill all Nephalem I don't understand.
If he wanted to do that then wouldn't he have voted against letting Sanctuary exist when the Angris council decided?
It's because he did not know what to do during the voting hence he was said to have went mad. He reappears now maybe because he finally has an answer.
I love your line of thought.
Malthael abstained the vote because Sanctuary and the Nephalem were an anomaly that went beyond his wisdom. He was the aspect of wisdom, and if he voted wrongly it would have tarnished his credibility as wisdom itself. He wanted to be sure so he sought for knowledge that would help him make the right choice; knowledge that drove him seemingly mad. Now, after all this time searching, he has his answer.
It is unclear if the answer is to annihilate the Nephalem, the demons that influence the Nephalem, both the demons and the Nephalem, Sanctuary itself, or something much more. Death, the end of all things, is a means to an answer, though not the only possible means, but a means nonetheless, that can satisfy the problem; the Eternal Conflict.