That is the problem with these vague terms that are used to describe poorly defined virtues, isn't it? Everyone can take whatever meaning they choose out of a term like "beautiful code." For you, I suspect "beauty" is nearly synonymous with "good". For the author, I think "beauty" was closer to "elegance." But there I go, defining one vague term with another.
You hit the nail on the head. Generally, it's counterproductive to allow emotional valence to overshadow the cold meaning of the words. For me, a statement like "this code is beautiful but unmaintainable" sounds perfectly fine and meaningful. But many people seem to have a vague cluster of "good" words, and when they're told that a certain "good" thing doesn't have another "good" attribute, cognitive dissonance ensues and they start making stuff up.