Motive: This one's easy. Although Wes kills Sam, it's possible Annalise blames Rebecca for his death. Plus, Rebecca threatens to turn all of them in, which would not only put Annalise's practice in danger, but her life too.
Evidence: Annalise knows Rebecca's dead, and she helps set up the whole "Rebecca escaped" narrative. If she's involving herself in the aftermath, there's a chance she's involved in the murder as well. Maybe she denies it to Frank, but she's a known liar. She'll do whatever she can to bend stories to her favor.