I'm sorry. (((Hugs))) You have to make your own decision. Is there a reason you haven't called Catholic Community Services or a women's shelter or a friend or family member for a temporary place to stay until you get things sorted out? I know Catholic Community Services has resources and you don't have to be Catholic to use them.
As far as your daughter goes, it might be more difficult for her if you keep going back and forth - but you have to make your own call on this. Remember, that you are the mom and sometimes moms have to do things that are difficult for their children to understand.
Sometimes it's best just listen to your kids and help them get their feelings out - my son's counselor told me this - it doesn't mean you have to change what you are doing. Let her know you understand that she is upset and that it's ok to talk about it, but going home isn't an option right now. Reassure her everything is ok and that you have everything under control - that you love her, that her daddy loves her very much and that she has nothing to worry about. Sometimes mommys and daddys can't be in the same house and that's ok. Tell her she'll see him soon enough and then ask her if she wants to watch a movie or snuggle.