It's a lot easier for me to think "what I would have done" with the benefit of sitting here with time to think about it, not on the spot, and under no pressure or stress. Don't beat yourself up over it, I'm sure it will pass and no one gave it nearly as much (or any) further thought. Sounds like you handled it fine.
Now, in my perfect world, I would have been cheerful, and with no defensiveness or anger would have said something like, "Since I was in the middle of talking with a patient when you asked your question and I wasn't focusing on the study protocol at that moment, I wanted to be sure to give you an accurate answer, so I referred to the protocol itself. I'll see if I can be faster with an answer next time." I would deliver this in a tone of trying to be understanding and helpful, but not at all apologetic or defensive.
It's probably unnecessary to set the record straight with your boss, but IF the opportunity presents itself in a completely uncontrived way, you could weave it into future conversation. Say this doctor does something else that raises people's eyebrows that comes up in conversation with your boss, you could say "Oh yeah, like that time s/he complained about me not having an answer about the protocol on the spot, when I gave him/her one in 30 seconds even though they had interrupted me working with a patient." Just don't act upset about it, wait for an opportunity to bring it up casually.