Jack killed her. Dean hadn't outright said it yet, but Mary knew it in her heart. Her last moments screamed death. Even if Dean never told her, Mary knew she had left her boys...again. "Dean...it's okay," Mary said softly, reaching across the counter to gently touch his hand. "I don't know, but I know I guess that Jack killed me...accidentally." She was still alive so he hadn't managed to kill her yet, but she knew it happened. Dean was pissed because he killed Mary and when Chuck, God, wanted to off him, Dean would have gone for it. Mary couldn't blame him; if something happened to Dean she would have wanted revenge too.
When Dean said he didn't do it, Mary was relieved. She knew in her heart, no matter what he thought of himself, that he was a good man. There was bad in everyone, but that didn't mean you couldn't have the right amount of good to weigh it out. "I'm glad you didn't," Mary replied softly. She reached out and touched Dean's arm. "I know how much you must have wanted too, but I'm glad you didn't, Dean. Even if it meant getting me back or whoever he offered."
Chuck was going to end the world and Mary wasn't there to fight with her sons. She took another sip from her beer. "That's a lot. A lot to know and be unable to do a damn thing about."