No, I don't think that you are overreacting. Yes, this has happened to me before; I was not asked by a white person, but by an Ethiopian man. He was absolutely amazed that I could not tell him where my family orignated. It made me sad.
How would I have reacted? I would have told the truth: that I didn't know. And I would have explained my truth. Yes, I would have said that my last name was probably the last name of a slave owner. I mean, would they really be surprised? They would have been uncomfortable, most likely. But no more uncomfortable than you were with the whole conversation.