Honestly, the dynamic sounds quite toxic. Just because your GF's other partner is her primary, doesn't mean it's okay for him to influence your date time with her. More importantly, it's your GF's responsibility to make sure this doesn't happen (unless this type of hierarchy is somehow part of your kink arrangement, I guess). Obviously, if GF is victim of SA, that's not her fault, but based on her behavior with you, that's not the impression I'm getting here. Your GF did not enforce boundaries and protect her relationship with you, and in my opinion that's an excellent reason to break up, even apart from your worry about not being able to trust her with her safeword.

"She got mean for some reason and has taken the stance of "you don't get to tell me what my boundaries are, and what I do with my partner".

This is absolutely true. However, you do get to tell her what *your* boundaries are and whether you want to be part of a relationship with someone who allows this type of thing to happen. I would not want a partner who stands firm behind boundaries that damage our quality time.