If the spoilered bit about the Emperor is true:
It just confirms one of two things. 1) You become evil with transformaton 2) Balduran was always evil. In BG1 you can troll the historian by telling them that Balduran sound like a pirate with good PR. Seems that might be right.
The Knights of the Shield are an evil organization in service of devil.
I still haven't finished the game but I will enjoy killing the Emperor when the time comes.