Why she was suspicious: At the beginning of season seven, it really seems like Mary Drake is running the show. She's the mother of Charlotte, and she's very angry about her murder, so there's motive. We also see her plotting with Elliott Rollins/Archer Dunhill to take all of Alison's money.
Why she's innocent: Mary saves Spencer in the finale, right after Jenna shoots Spencer. Mary then tells Spencer that she is her real mother as she is bleeding out. Not only is it far-fetched for Mary to have tortured her own daughter, but the real "A.D." drags Jenna away while Mary stays with Spencer.