Counseling for the kids would probably be a good idea. Is there any set visitation? Maybe supervised visits through the courts too. That way the kids get to see their dad and you will know that the visits are safe.
I have never been in this situation but have a friend who was. Her kids were extremely angry at her for a while but once they got older they realized their mom was just trying to protect them and they thank her for shielding them from the craziness. It will be hard for a while but as long as you're doing what's best for the kids everything will eventually work out.
Hang in there!