User blog comment:ArthurMerlinLancelot/FINALLY/@comment-5684105-20121216072859/@comment-5684105-20121216225538

Knightofthecart, Morgana DID know in 2.02 why Merlin had poisoned her. In 2.01 she told Merlin, "It's alright, Merlin. I understand. You were just trying to protect your friends, I would have done the same...I was so naïve, Merlin. I don't think I really understood what I was doing. But, believe me, I have seen the evils in this world. I have seen firsthand what it is that Uther fights against. You don't know how much I regret everything that I've done. I just...hope that you can forgive me."

She knew why he poisoned her. She said it; she wasn't just making up something on the spot so Merlin doesn't suspect her anymore. The only thing was, she lied about being sorry for it.

So, yes, she did know. And from what she said, Merlin knew she knew why.