You make it sound like it was an accusation. It's not. Enjoying food and cleaning your plate is a good thing, and a compliment to the restaurant.
I think in this case "What an interesting assumption" would not have been a very nice thing to say at all, because it would sound like the meal hadn't been very good at all.
And you say he was speaking "enthusiastically". That means he was glad that you had enjoyed the meal. He takes pride in what he serves! (Though he didn't cook it himself.) Maybe he likes that dish too!
I'd actually be much more annoyed by a waiter who brought attention to the fact that I had *not* cleared my plate - I'm always a bit ashamed when I accidentally order more than I can finish and end up wasting food or looking like I don't appreciate the meal. (Take-away bags are not really "done" in most of the restaurants where I live.)
Edited to add: a good response for this waiter would be simply: "Yes, it was very good, thank you!"