Her role in other meetings still seemed mostly administrative. This was an unusual meeting, and Joan's trivial partnership share was inconsequential from a decision-making standpoint. I think putting her there, on Thanksgiving morning, was a way of showing her status with the other, more powerful partners, as well as a callback to her tirade against Don for making unilateral decisions that affect the rest of them. She's part of the team deciding his fate, even though he owns at least 5 times as much of the firm as she does, and was once considered indispensable to the firm. The scene doesn't say outright "Joan landed Avon," but the fact that she's there in consistent with her being successful and treated as more than "just a secretary," as she had earlier complained to Kate.
I think her role at partners meetings stopped being administrative when she started being a partner and they got someone else to take the minutes--that was the signal that she now had a seat at the table. I think her being there at the end definitely showed that she was part of the team deciding his fate despite her only owning 5% but I don't think it had anything to do with Avon--she would have been there regardless, imo. Joan's feelings that she was treated like a secretary weren't, imo, about how she was treated at partners meetings but about how she was seen in the office in general.
To me it seems like, if she *hadn't* been there it would have been a signal that she was being disrespected and not considered a real partner, but her being there was just business as usual, as it should be. That Ted and Pete weren't there seemed like a sign that SC&P West was a real thing that was happening and their attentions were already focused elsewhere.
I do think Cherith has a point that her position fluctuates--but I think that was also a story thing. Joan felt like her place at the table wasn't really secure in the sense that she wasn't really considered valid (as opposed to Pete who was insecure because he saw everybody wanting to push him out). I think we're now supposed to know that Joan was supposed to have gotten over those feelings of insecurity, presumably because she proved herself with Avon, but of course, that wasn't clear when last we knew she was still in limbo hoping the guy would call. I have no problem with Joan working on Avon not being an actual story since Joan being triumphant and awesome is more of an ending than a story in itself, but I honestly don't think there were any real clues we could have been expected to pick up on. I don't even think MW meant that, he somehow just meant that we'd know that he meant the story to be a happy one rather than a sad one--but how would we know that?