Board Thread:Spoilers!/@comment-26612471-20150719193843/@comment-26116863-20150719194748

Well, we know that Killian has been struggling with his dark side. We saw that he was still capable of doing evil deeds when he thought he was being controlled by the "evil hand". He likes having a reason to be bad, and up till now Emma has largely been his only reason to be good. So it seems likely to me that he could at least unconsciously allow himself to be manipulated by Emma, even if deep down he suspects what she's doing. He might even openly go along with her plans, justifying it as an act of loyalty and love.