One thing that no one has mentioned is the public relations risk. According to the LA Times story, 3 woman gave interviews to the investigators and provided evidence, including at least 1 video apparently. Potentially, there are other women that gave interviews in confidence and will not go public.
So MLB is in a tough spot, they give Bauer a light suspension, say 40 games and they run the risk of having a public relations nightmare with news stories about Bauer's bad behaviour, that MLB was aware of, popping up. From a business perspective, MLB probably didn't have any other choice but to do what they did.