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I guess the reason why Mary was able to leave Salem is because of the "body swap". Since the Countess had Mary's original body when she was killed by her daughter that would mean the body the witches resurrected was the one that decayed towards the end of the episode. So basically if the Countess was to leave Salem with that body she would have died.
And btw the episode ended very nicely, if they were to drag it any longer the story would have been thinned out and eventually would have become bo