The Emperor is neither good nor bad but neutral; maybe leaning toward evil. Only because he is manipulative in the information he gives you and when so that it has the most influential effect, at least the information is true. He does not hide from the fact that he is Balduran, the founder of Balder's Gate nor that he was put in the position to survive or die with his friend, the dragon. Or that he lived in Baldur's Gate for many years not very long ago in the storyline. Although now, he does believe he is better even than the Absolute and wants to become the next God rather than just wanting the freedom he consistently wants you to believe is all he wants.
As far as Orpheus goes, he is definitely the good side here and he will turn himself into a mind flayer to save everyone from the Absolute. So either way, on this choice you're saving your relationship with Lae'zel and the Githyanki people.
