M., the only person who can tell you what to do here is an attorney. However, in my experience as both a homeowner and property investor, I can tell you that she's not the homeowner so she's not responsible for the roof repairs nor in any way responsible for repairing the house in preparation for a sale. Unless, of course, she and the owner already has a prior agreement for her to do this. The owner apparently knew she was sub-leasing or else he wouldn't have called your husband (how would he know to if he thought she was the only one living in the house?)
I would go over your lease agreement with a fine-toothed comb and question every single word in it. This is what an attorney would do and a judge would look at. I worked for 6 Superior Court judges in AZ for many, many years and can tell you that a judge is harsh on both parties so prepare for both the best outcome and the worst. Know the law. It's your only defense.
The owner apparently also knew that she was having money issues or wouldn't have cautioned you not to work with her. The owner is knowing more than he/she is saying and 1) has just caught her in these lies or 2) knew about the sub-lease all along and was working with her on it. Now that the sub-lease has blown up in both their faces, they're forcing you to pay.
Do you have receipts for the rent? If yes, then make copies and send to the owner. If no, then you'll not stand much of a chance in court as you have to prove you actually paid the rent.
If it were me, I'd sue both of them for wrongful tenant/landlord agreements that you knew nothing about and that is causing harm on you and your family. Something's really fishy about both these characters and I'd let an attorney who specialized in tenant/landlord disputes work it out for you. Most atty consults are free for the first 30 min and I'd talk to several to get several points of view.
If an attorney can't help you (or costs too much), at least with the knowledge you've learned from each attorney you can go to a law library (most universities have one or check with your local library) and draw up your own case against them. Filing is easy and it doesn't matter if she's in another state - the property is here so the law for your particular case falls under GA law.