And surprise surprise, the moment Orpheus is freed, he is actually pretty reasonable, aside from few accusations.
He literally says he needs you, that he's obliged to overlook your transgressions, but that really you should've offered yourself up to his honor guard to be killed for being infected. An honorable death to him.
Not so much reasonable as that he really needs you as much as you need him.
Regardless, all Emperor had to is wait it out and see if Orpheus' hatred towards him was stronger than his desire to kill the brain (both of 'em share a common goal after all, they just go about achieving it differently) and free his people.
That wouldn't have been in character for The Emperor. He doesn't gamble with his life, which you can see if you try to kill him at the behest of Vlaakith.
