I like the rehab theory. I think with Rossi's return (there's history there, even if it's not romantic, but I think it might be), what she's seen in the field, the trauma she's experienced with the team because of Foyet and Doyle, and the pressure she receives from the director in regard to the team, I can easily imagine her turning to the bottle.

Oh, also... I believe when she told Hotch she was taking some time for personal reasons, she said she might need his help covering for her. Why else would she need his help at that time, if not that she was in the middle of something that could get her in trouble?