Outcome: Confessed to crimes and executed, most likely hanged
Actually, in legendary minister and witch-hunter Cotton Mather's Magnalia, the record says of Johnson, "And she died in a frame extremely to the satisfaction of them that were spectators of it," which sounds pretty final and most likely unpleasant. Mather also reports that "upon the indictment of 'familiarity with the devil,'" which came on December 7, 1648, Johnson "was found guilty thereof, chiefly upon her own confession," including having murdered a child and other evil acts. Based on the methods of interrogation of the time, it seems as though she was probably "coerced" into her admissions (red-hot irons, scalding water, etc.). It also appears that Johnson was first arrested for stealing and whipped for that crime before her witchcraft trial. The record also states that she gave birth to a son while in jail awaiting her execution, and that the son was "bound out" (or indentured, as a servant or an apprentice) until he was 21 years old to a Nathaniel Rescew, who was paid 15 pounds to take care of and educate the boy.
For a while, it was believed that Mary Johnson had been the first to be executed in New England for witchcraft, but subsequent evidence seems to point to Alse (Alice) Young.