I think Scott believed Theo because he still hasn't forgiven Stiles for what happened when he was possessed by the Nogitsune. Knocking Kira out, stabbing Scott in the stomach, hurting the coach, blowing up the Sheriff station, having the Oni kill Allison, etc. I think Scott deep down knows it wasn't Stiles that did those things but because the Nogitsune looked like Stiles, he has a hard time seeing them as separate being, if that makes sense? Like, he thinks of the Nogi but sees Stiles face.
Yeah I’ve heard that reasoning a couple times already. Someone said it’s the reason why Scott flinched away from Stiles. It seems like a logical explanation. But so far there wasn’t any canon mention of this. And even if it’s the truth it would still be pretty awful on Scotts side. Stiles was as much of a victim as everyone else, if not more.
Would‘ve been interesting to see how Scott would’ve dealt with Jackson after the whole Kanima stuff cause that’s practically the same situation, someone being used to harm others and then being the face that’s associated with those awful events. Too bad we won’t ever get that.
But yeah. It could be an explanation. Some people even think it goes further back and Scott blames Stiles for dragging him into the forest and ‘getting him bit’ thus starting all of the supernatural disasters. Which is also a horrible reason.