But suggesting to consume Orpheus' brain provided narrative evidence that he was, in fact, a mind flayer with a mind flayer's desires, and his perspective had indeed been tweaked too far from the human template to be trustworthy. And for the whole game, the story told us that being mind flayer meant to lose ourselves, and the Emperor, by this event, proved that to be correct. Apart from that, the story provided no in-world evidence that this was necessary. It was just the asserting of an entity whose words we could no longer trust. Acceding to the Emperor's demand thus feels like crossing a moral event horizon, the most significant act of unnecessary evil in this story.
I think it would be unreasonable to expect the Emperor NOT to be a mindflayer. Biologically, he is one and needs to consume brains. Even so, I am certain he has not lost himself. I think the game has made it rather clear that he is an exception, a unique mindflayer (in the words of the Narrator). What the game seemed to underline for me was that mindflayers in general lost their human side after transforming -
but there are exceptions. It is possible for the human's consciousness to continue. After all, Ansur recognises Balduran in the Prism. Withers recognises us if we transform. There are always extraordinary individuals, and there is always hope we can rise above our nature.
Regarding the ending mechanic, we know we need Orpheus' power to resist the Netherbrain, plus a mindflayer's mind to dominate it. You may distrust it, but in-game, there is no option not to proceed without a mindflayer. I think that supports the argument that the Emperor's assertion is treated by the game as fact. You can say that it's a lazy way to write a plot, but we already know they were pressed for time in Act 3.
Anyway, my reference to Orpheus being the son of Gith is not a strawman, because the game is forcing us to choose between Orpheus and the Emperor, and is clouding the issue with questions of trust. I find it surprising that players are so willing to trust a person whom they know next to nothing about, save from some Githyanki propaganda disks, and to betray the person who had in fact been with them the entire journey, guiding them through the process needed to destroy the Netherbrain.