I think you'll be fine. Managers just need to know about these kinds of things. As long as you did the right thing, there should be no problem. I would suggest in the future when a customer gets upset to run it by your manager, even if you think it was nothing. That way, they have your side of the story first-hand and can deal with the irate customer. Your boss cannot back you up if they don't know about the incident until the customer bombards them with it later.
At my old pet store job, people threatened to call my boss a couple of times. One lady threatened to call corporate on me once. I was busy checking out a line of people and this little girl comes up, interrupts me as I'm talking to a customer, and asks if she can hold a rabbit or something. We have every right to say no, especially if the customer wants to touch, but not buy. We aren't a petting zoo. But it was a Sunday and I was feeling kind, so I told the girl if she could wait for a couple of minutes, I would meet her over by the cages. I get through the line of people, start heading over to the rabbits, and this woman comes up to me and asks me how I could say such a thing to her daughter. She throws the products she was going to buy on the counter, asks for my name, and says that corporate is going to hear about this. I was so stunned and terrified at the time. The girl obviously misheard me and the woman gave me no chance to explain myself. I told my boss immediately. She understood and said that I did nothing wrong. I hated my boss with a passion, but she said that she would always have my back as long as I did the right thing or came clean when I didn't. I think that is all any boss wants. They know that people are difficult and hard to handle.