The real answer is no there are no agencies that will help you financially to do anything about getting out of an abusive relationshipIf you are not divorced, you can leave with your children since you are their parent. There are agencies in every town (ie Traveler's Aid, Salvation Army) that can give you help and advice for housing until you get a job. Money for food and gas to get there and until you make a connection would be needed. If you have an idea where you are going, perhaps you can do some research on the Internet. However, I advise that you do your search at a library so that the history of your search is not on the home computer.
I know in the UK women's AID can give you a lot of help to relocate within the UK, but frankly the UK is smaller than many US states.
There are a LOT of problems under Federal Law with transporting minors across state lines and I don't think anybody is going to touch such an issue..
You need to see a lawyer, I would say that if you can get a court order permitting you to return to Indiana with your children, THEN you may find you can get help, but recognised agencies CANNOT afford to help you break the law.
Have you considered relocating WITHIN Montana?