You feel those things because you love him. That's fine. You can love him and not allow him to make you miserable. You say you are already separated. That's one advantage you have. You don't have to live in the same house with him and can control how often you see him.
If you don't think the marriage counseling is working, then quit. It doesn't really sound to me like you are all that interested in living with the man. Your main fear appears to be your children. Let me tell you one thing. Your children will be fine. It's better to come from a broken home than to live in one. Your children want you to be happy, even if that means you and their father don't live together.
Welcome to SR! You'll find a lot of support here.