I had a similar living situation. It was supposed to be four women in a house, but it turned into three women and a couple. It was extremely awkward and uncomfortable. Here is how it was resolved. We spoke to her about him living there numerous times, but he continued to stay. He was a nice enough man, but it was stressful since we hadn't expected this living arrangement. One weekend when they were away, her mother called and another housemate told her EVERYTHING! They moved out soon after.
So I think that you should talk to your roommate. If she doesn't stop this situation, tell her mother.
Or maybe not.