I think Peggy was kinda zinging Joan for having slept her way into a partnership, yeah - but I also think Joan really, honestly, believes Peggy slept with Don at some point. That's been a thing from as far back as Season two, hasn't it? And I don't think it was ever resolved, or even brought up in front of Peggy until this episode. Part of the reason I liked that exchange was due to the fact Peggy finally got it out there, because I also interpreted it as YEARS of her knowing people at the office thought she fucked her way into her position, and those people likely thought that BECAUSE of Joan's backbiting, and she finally got that out there to Joan's face like "No. *I* didn't..."