I agree with RuffRuff on this one. If anything, you helped the owner by giving the impression that he is concerned about his customers and meticulously honest about the contents of his products. Yes, the caller was looking for gluten-free cones now, but the next time she is considering purchasing bakery items she’ll remember that when she called this bakery she received an honest answer. And since she was looking for gluten-free items for her daughter’s classmate, chances are she generally is not concerned about gluten. (Even people with a gluten-free family member don’t necessarily serve only gluten-free products at home–we don’t).
minor nitpick: it’s called gluten intolerance, not gluten allergy.