In this case, I don't think the game is actually relying on plot armor. Here's what the dialogue is:


Narrator: *The brain is on the cusp of its final thought. And it's taking all of Orpheus' strength to keep it there. An opportunity perhaps?*
Player: Go ahead. Command the brain to destroy all tadpoles and then itself.

So, Orpheus issues the command to the Absolute to destroy only the tadpoles and then itself which the Absolute must obey. The Absolute's death appears to trigger a wave of psionic energy which leaves the mindflayers under its command temporarily stunned or impaired. We then see the citizens of Baldur's Gate finishing the mindflayers off, which is why all the other mindflayers are dead at the end.