Mostly adding to what has already been posted:
Why is there already so much sin on both sides?
This is a serious issue and worth in depth examination by them, if either is willing. It sounds to me like neither of them are followers of Jesus Christ. The fact she even talked to her pastor is a good sign, however, people that have been raised to be afraid of condemnation might do this whether they're genuine followers or not.
What the best course of action is for her is very dependent on the things she's been through in the past and what other things she is dealing with at this time (e.g., blood relative issues, financial issues, etc.). There is no way to be sure any advice will apply (without the person knowing her). If her pastor has been pastoring for 15+ years, he is potentially her best advisor.
Trying to understand what God wants in situations where everything involved is sinful can be impossible. Fortunately, there is a best choice, and that is accept that all choices will lead to pain for a while, give up everything that "I" want, and do everything that God wants. While this is much easier said than done, I believe this would please God a lot and may be the only fast track to having a clear conscience. All sins forgiven and forgotten. A new start, if you will. Anyone that genuinely wants to do this and acts on it (regardless of how successful they are) would be doing something pleasing to God.
Ideally, both would get into Christian counseling (if not psychotherapy + pastoral counseling). However, by the time someone posts such problems on the internet, these sorts of avenues have often been tried or rejected already.
From trying to separate the issues so they are each easier to understand:
Abuse
I don't know what constitutes abuse in this situation, but if it really is a clear case of abuse
that won't stop, it may be a viable option to separate or divorce. If it is the sort of abuse where she needs to get a restraining order, then she needs to act to protect herself. (In populated areas, there are options for people who can't do this financially; counseling that specializes in that situation is advisable.)
His Adultry
For the purposes of simplification, if he is no longer open to trying things to save the marriage (like ceasing his adultery), I think this can be viewed as part of the abuse.
Her Adultry
As hard as it may be, if she is seriously concerned about what God thinks, she needs to stop seeing the other man. It doesn't matter that his divorce is in progress. She is married. He is married. If she is separating from her husband, she needs to choose to be celibate for the time being. Right now she is finding comfort from the pain in her life from this relationship, but she needs to seek the comfort that comes from Jesus if that's the relationship that is the priority to her.
It sounds to me that it would be beneficial if she were able to recognize that everything is screwed up right now, spiritually speaking. Jesus will make a way out for her, but she needs to be obedient to experience it. It might take longer than she wants for it to be resolved, particularly since it sounds like the Lord needs to help her with her own internal conflicts.
Life can be impossibly difficult. If her situation is affecting her like that, then the Lord's grace is available. He died to forgive her of all of her sins. Anything she does in an effort to be obedient to please the Lord Jesus Christ will be successful in pleasing him. Genuinely asking him for help and yielding to him and doing what he says would be a good path for her. The Lord knows her limitations and the consequences of all the choices before her. She may already know what He wants, but it might be good to double-check it with her pastor.
Show me one Christian program set up to ... help her raise the family properly with no husband in the home. All such programs are secular only, there are no Christian ones.
I'm glad to report that our church has something like this (but it's not comprehensive).