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.
We actually know quite a bit about Orpheus. We know he is a githyanki, which means he is 1) fiercely loyal to the cause and 2) really, really doesn't like illithids. These two things suggest that Orpheus can be a potential, and a rather useful ally.
And if we choose to not immediately dump a potential ally, we are betraying the Emperor? Even if he is right and Orpheus will attack as once freed, we can just kill him and let the Emperor eat hsi brain. There's literally no reason to not free him, other than the Emperor being a bastard, which he was throughout the entire game.