No, he literally says "Hurry! I've got one of those brain things cornered! There, in the grass, you can kill it, can't you? Like you killed the others." And the the knife scene. Why would he try to get our help at killing the brain thing if he thought that we were WITH the brain things? He didn't think that we were under midn flayers' influense.
Because the scene has been rewritten and now his reasoning is inconsistent? He says that to distract you, but then when you've tussled he accuses you of being a thrall, because he saw you walking around the ship.
There's also a theory that the mind-flayers are in the middle of a civil war, who knows, maybe he watched thralls and intellect devourers killing each other.
