Hmm, I don't know. My theory is slightly confusing but here goes.
The timeline was cut very close. Rebecca had to be killed in between Wes and Annalise going to find her, and in between was that scene where Wes delivers his final defense for Rebecca AND EVERYONE IS IN THE ROOM. Then Annalise goes to find her and everyone else is still in the room up to the point where Annalise yells that Rebecca is gone. I assume Annalise runs up the stairs and out the door and everyone follows her except Wes, who goes to look at the empty chair. This means that Wes or Annalise had something to do with her DISAPPEARANCE FROM THE CHAIR (not her death!)
Here's my theory. When Annalise goes down to "ask her nicely", she actually MOVES Rebecca to under the stairs, bound and gagged, and pushes the boxes against her so she can't be found. Then she pretends that Rebecca has escaped and the Keating 3 (minus Wes) are all seen outside (IIRC) with Annalise. My theory is that someone who knows that Annalise hid her there killed her. I think Annalise, Frank (maybe Bonnie too but it hardly matters since Bonnie seems able to find things out) worked out a plan to tell the Keating 4 Rebecca escaped while they figure how to deal with her. Annalise and Frank are both at a loss about dealing with her earlier in the episode so maybe they just want to buy some time and keep the Keating 4 close and on edge.
Now for the actual killer. It has to be Bonnie for this theory to work. I think Annalise and Frank were completely honest with each other when they said they didn't do it. Bonnie could do it too, while the Keating 3 were outside and Wes was on the stairs. (I think there was some buffer time in between all of this when the Keating 3 retires to their homes and Wes gets guilty. This leaves plenty of time for Bonnie to kill Rebecca and Frank and Annalise to move the boxes and find out she is dead but not by their hand. They also don't seem particularly surprised she's dead and aren't really worried about the killer because they know it's Bonnie, the only other person in on their plan!