No matter how one turns it around, the main character is a bad person too by definition then because in order for them to live, someone who doesn't deserve it must die.
That is the narrative of every living thing on Earth. Life feeds on life, innocent life or guilty life. So when broken down to that level the character and the player aren't meaningfully different. While typing that, a handful of presumably perfectly pleasant peanuts who were killed as feed for their overlords possibly weeks or months ago finally came full circle and delivered their delicious calories to me.
But lets not get too far down that rabbit hole. As I mentioned earlier, based on the Emperor's actions, there is no way to clearly distinguish if his plan was in fact his own, or if he was playing a role assigned to him by the brain. As soon as his plan goes up in smoke he joins the brain, without hesitation. Abandons 'his?' plan rather completely and this exposes (in my opinion) that he was never a free mindflayer at all, just a tool of the brain whose mission had failed. He then is found fighting to protect the brain, not to protect his freedom, not trying to find another way to bring his plan to completion.
I don't believe that result was the act of the free soul of Balduran in Illithid form. I believe that was the final unravelling of the Absolute's agent.
