Why She's Guilty: As Mona tells Spencer in the premiere, she's still very affected by the dollhouse, and she still has nightmares. She has plenty of reasons to want Charlotte dead. Plus, she's been on the "A" team before.
Why She's Innocent: Now that she's getting into politics herself, it's entirely possible Mona doesn't have the time to be a technologically advanced supervillain. Plus, she really seems to have changed so much since she first went crazy, right?