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.

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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).