Fair point that we don't know how the whole Orpheus thing will turn out. From a good-aligned perspective, my biggest problem is that we have to side with the Emperor without even talking to Orpheus and giving him a chance to help out. If we were able to let him out and he then refused to cooperate with the Emperor (or they refused to cooperate with each other) then to my mind there would be more of a choice to be made there.
From the in-game info such as what we find in the creche and what Orpheus says when freed, I do think the impression he gives is positive enough that a good-aligned character would, for me, need to be imagined to either be suspicious-minded or to have knowledge of the githyanki that's not presented in the game (both totally valid RP options!) to find it easy to side with the Emperor over Orpheus. But if the Emperor were less unreasonable about flouncing off in a huff just because we insist on talking to Orpheus, then depending on the relationship that had developed over the course of the adventure could well be enough to swing things in his favour if the two refused to work together when they both had a chance.
