I am very passionate about the lack of logic in the current ending so I'm going to post my thoughts
Emperor should absolutely not side with the Netherbrain in the case of the true souls freeing Orpheus. Siding with the Netherbrain means it loses its freedom, which is exactly what it has been working against the entire story; That is the exact opposite of what it wants.
I agree, it's incredibly jarring when the Emperor makes that decision. And makes even less sense when he shows up at the final battle against the very team he has personally seen squash enemies against all odds and under any circumstances. In these two instances he goes against everything the game has been telling us about his character, that he values self-preservation and freedom above all.
You made some very good points. A character who has been supportive of the Emperor should have the ability to persuade him to trust us to protect him against Orpheus.
