Should you let the emperor assimilate Orpheus?
To summarize, players should side with the Emperor if they don’t want to become Mind Flayers, and they should free Orpheus if they don’t mind all the tentacles. The former may cause Lae’zel to turn against the player, and it will force Karlach to return to Avernus so her Infernal Engine doesn’t cause any more problems.
What happens if you side with the emperor?
By siding with the Emperor, you’ll give the Netherstones to the Emperor. In the end, this means that he’ll fight the brain with you as an ally and then depart in the end, disappearing from the eyes of the world for the foreseeable future.