The fact that you expressed your hurt and concern about all of what went on, and you have only been met with anger is NOT okay. It is yet another layer on top of the already pretty terrible circumstances that Emma committed sexual assault/rape against two people and violated their consent, and then pushed your very reasonable boundaries around safer sex, knowing that she holds a position of power over you as a work authority figure.
1) Just because you had unprotected sex with her once after her escapades doesn't mean that you have to keep doing it. If you're not going to end this relationship (which is my first recommendation, but one that you don't seem to want to hear), then at minimum, you should go back to using condoms, as you clearly can't trust Emma to be safe, but you also can't trust her to not push your own boundaries.
2) Please work on changing positions, or whatever you need to do so that she is NOT your superior at work. And please consider this a lesson learned to never date a work superior again, ever.
3) Therapy, individual for yourself, to potentially work through your feelings and boundaries, as a couple to work through communication and boundaries, and sounds like Emma definitely needs individual to work through her issues around drinking and pushing herself onto people and violating consent.
Again, I strongly suggest that you reconsider leaving this relationship. You seem to be focused on the fact that she's otherwise a lovely person as a reason to stay. But remember, this person sexually assaulted two other people. If your best friend, sibling, parent, anyone that you really deeply cared about came to you and said that their significant other violated the consent of two other people, and then did the same to them, what would you recommend they do? And once you think about that, why are you giving yourself a pass on taking that same advice? You can deeply care about someone and still realize that they are not a good partner and not someone that you should be with. It hurts, it's hard, but you need to take care of yourself.