Bad reference from PhD supervisor
Given what you describe, I think you better not include your supervisor. Her recommendation will be the most dominant because she knows you the best. Given that in the best case you will get a mediocre recommendation, and in the worst case even a bad one, it is not worth it to include her. 

Do not include her, but be prepared to explain why you do not include her. This explanation should be convincing, but not too damaging for you. For example, if you just say that you had conflicts with her all the time, your potential employee might conclude that you are a conflicting person.