Sometimes people make comments as a way to blow off some steam and not realize how much those comments hurt and dig deep. It sounds like she's willing to work things out but 2-way communication is vital to making your new situation work. Joint counseling sessions might be good too but I agree that it should be someone that's familiar with gender issues but also family issues.
These types of conversations are never easy, and difficult to start. But the talk is worth having, and I hope you can sort things out and continue your life journey happily together.