Is it safe to assume you live in America?There are several reasons why she may be staying. Most of them having to do with a victim mentality. A part of her may also feel like she has to stay to protect her children. The best thing to do is stage an intervention, even if it means getting police involved. If the kids can stay at the sister's house then that would be a good temporary solution. She then can get legal action against the father for the time being, a restraining order preventing him from getting close to the children, and getting to the house.
An intervention would be needed. Time away from him will definitely help her. Family getting involved now, (in a supportive manner, no "I told you so" type of attitude), would be ideal, and possibly the only way she can be free of him.
I'll pull some cards later for insight or advice. Please update. The safety of the children is the most important thing. I may be just morbid or expecting the worst but my first thought was that he may sexually abuse his daughters at some point.