Joan is having an affair with Grace Berk. They meet at the Sunset Palace Hotel at 1:30pm sharp every Tuesday and Friday. Rita has known of this affair for some time, and used it to keep them both in line for an unspecified amount of time. When Alma discovers the affair, she blackmails Joan into dropping out of the running for president of the Garden Club, making Grace leave the club altogether. It is likely Joan leaves with her, although this is never confirmed.
In The Unguarded Moment Joan makes it clear that she despises Rita, implying that any friendly behaviour seen earlier in the series was merely a ploy to stay on her good side due to the compromising information she had. Alternatively, it could be that she is so disgusted by Rita's former life that her opinion of her changed entirely, but this seems more unlikely.
Joan never seems particularly fond of Alma, but after she reveals her true capabilities in the penultimate episode of the series, Joan appears simultaneously scared, and angry with her. She immediately goes to Grace to warn her of Alma's threat, speaking with tears in her eyes.