I don't think Mary knew about the plot to murder Darnley, but I think that she did what she could to cover up the crime afterwards, which was a terrible mistake. Even Queen Elizabeth seems to have sent Mary a warning that those people who were responsible needed to be held accountable. Elizabeth had been through a similar situation herself after the strange death of Amy Dudley, the wife of her beloved friend and advisor, Robert Dudley.
I believe that Mary married Bothwell because she was pregnant, but I think it was a mistake for her to do so. Her marriage to the man most people held responsible for Darnley's murder blackened her reputation in Scotland, and directly contributed to the loss of her crown, and eventually, her head.
As a Catholic, Mary couldn't get a divorce, but I am surprised that Mary never tried to have her marriage to Darnley annulled. When they were married, they did not have a dispensation to do so, though they were cousins. They eventually got a dispensation, but it seems to me that the question of the dispensation could have provided Mary with a convenient pretext to boot Darnley to the curb with the sanction of the Pope, making his murder unnecessary.