It seems like her issues are with being a "homosexual". I've run into this several times online of late and I just don't understand it either. She may not give your BF a pass because she assumes he can't have a penis and that's a mandatory feature of being "male" -thus the headshaking and incredulity.
Actually, this has all the hallmarks of your typical Christian, "I'm going to save them" intervention. This would explain why she felt privileged to delve right into your deepest personal business and then be disrespectful. They typically start with the one on one lunch invitation and then spiral out of control fairly quickly. There must be a handbook on this somewhere where they give instructions on how to turn us away from the devil...or dikes, or the gay lifestyle, or whatever the case, lol.
It sounds like you handled it pretty well. Bravo.