No, Brian did indeed kill the evil sadistic clone but the 'Thriller' inspired ending was to indicate that there is still a little bit of evil in Stewie and he hasn't gone soft.
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I think he did because stewie looked evil at the end of the episode. I think he did because the evil stewie was happy when he made the creepy face
he asked a question only the real stewie will know
Brian tell Stewie the truth when they are stuck in the bank vault in the episode Brian & Stewie
All of the "Road to" episodes are primarily Stewie and Brian centered episodes, also of the episode titled Brian and Stewie
Stewie told Brian he had killed Seven babies.
No, Stewie Griffin only loves Brian.