At this point I don't think her telling the boss to stop is enough. I think this is enough to end at least 99% of relationships. She clearly understands she crossed a boundary, yet she insists that she didn't know what she was doing. She's making OP feel bad about himself, despite her being 100% in the wrong. She's still lying to him. She's basically revealing as little of the truth as possible and then telling OP he's overreacting.
This is toxic behavior, no qualms about it. If it was me, this relationship would be over. If OP is extremely forgiving and wants to help his GF improve as a person he could make an attempt to stay with her. She needs to immediately file a report with HR, cut off all non-business contact with her boss, and enter therapy for whatever issues caused her to think this behavior is remotely ok for somebody in a relationship. Barring all of that, plus a profuse apology, I don't think there's hope for this to return to being a healthy relationship (if it ever truly was).