THAT IS a reasonable attitude. The OP sounded a bit too much on the white knight side of things, but this message is spot on. Actually not quite spot on.

All you can do is apply reasonable efforts towards her being alright and feeling safe with you. You cannot change her past, cannot be her counselor, etc. So "make sure" - no, you cannot make sure. If you expect making sure of yourself, you might already consider this enterprise a complete failure and might as well part ways with her on cordial terms right away.

You demonstrate a slight bit of B&W thinking when you say that you do not understand why she talks to her dad when he phones her from his jail cell. You seem to be a little too much of the "either or" conviction, but, hopefully, you will mature soon to appreciate the complexity of human relationships. Plus, you have never been in her shoes. You do not have a dad who is in jail. You really cannot imagine how it would be in her shoes. So stay out of it as much as possible, focus on today, and let her and her counselor figure things out. If she does not invite you to a joint session, so be it - her private past is her private past. That the counselor commented positively on your gf's progress since you guys began dating is good news, but much more progress would need to be made because so much early trauma happened in the life of your gf.

Make sure you continue being engaged in the activities you enjoy. Make sure you do not become a rescuer. You still have your own life and path.