I actually think the whole experience was a great opportunity for your son to learn that some people don't respond well to being labeled, or having comments made about their body. I think you overreacted by getting so upset about it. If someone's feelings are hurt and they tell you, getting defensive or upset about it isn't really the right way to go, or the right behavior to model for your son. Yeah, it sounds like she was unnecessarily harsh, and she'll probably get a good talking to from her boss about that. But from you, a profuse apology to her, and a learning moment for your son was in order.
We have a flat rule that our family doesn't make comments on other people's bodies. I tell the kids that if they have questions or want to talk to me about how a person looks, they can do that when we're at home, and I'll answer all of their questions honestly. I've explaind that people's feelings can get hurt when you comment on their appearance, and that the only comments we can make about or to someone are those of the "What a lovely dress!" and "I like your hair today," variety. My son is still learning, at age 6, and has a hard time not staring at people who look very unusual, but we keep practicing. If I notice him staring, I'll talk to him about it later, and ask whether he has any questions.
I don't think it's too late for you to seize this opportunity to help your son understand the correct approach when he sees someone who looks different in the future. I'd probably wait until bedtime one night, and maybe show him some medical information about dwarfism on the computer. I'd ask him if it scared him when the woman spoke harshly to him, and comfort him in that regard. And I'd explain that she was born with a small body, and probably gets grumpy from people commenting on it all the time, so she wanted to correct him when he used a word that upset her. I'd also explain that it makes people very happy if he smiles and says "hello" to them, without acting as if anything about them is unusual, because people who look very unusual rarely get that sort of response from other people.