Oh man. XD He wasn't thinking constructed thoughts a lot; there was a lot of HOLYFUCK startled awake!! feelings and also he started out already angry from the unsopored nightmares. when he saw John standing between him and Noir he did get a jolt of "what is he doing WHY (i know why oh god)" but in the middle of all the troll-adrenaline he pretty much just immediately reacted. John trying to help good, Noir trying to hurt them bad, here's your target!

Later he berated himself quite a bit for siding with John so instinctively. I mean, okay good, yes, the guy apparently has your best interests at heart, but your reaction to it could have been a little more deliberate/logical/calculated!