I firmly believe that Lexie managed to kill her father – presumably foir what he did to her that was to take her away from her husband and son.
EJ most likely saw this and cleaned up after her. That is why he KNEW that Will did not have anything tio do with the murder.
There is always a twist in Salem murders – and this seems to be the best oine since noboidy will go to jail – again a Salem "tradition."