I like both of these ideas. The fact that Dr. Rappaccini "created" a garden and poplulated it with a created Adam and Eve certainly does more than suggest the idea of a scientist playing God--and the detrimental and even deadly consequences of doing so. It's true that Beatrice is representative of all things beautiful (art and literature and music and all natural beauty), and that's certainly an evident point of view in this short story. Because it's the evil manipulation of science which kills beauty, I have to think that's the dominant theme.
Contemporary critics of Nathaniel Hawthorne felt that Dr. Rappaccini was based upon Dr. Robert Wesselhoeft, whom Oliver Wendell Holmes denounced as a "quack" for his homeopathic medicine. Certainly, as a Romantic, Hawthorne would be inclined to denounce the advancement of science in tampering with humans. So, there seems to be a theme of Science vs. Nature.
If I had to sum it up in one word, I would say the "sublime." That is to say, in the Romantic period one of the ideas about art, beauty, and nature that circulated was the idea of the sublime: a natural phenomenon so striking that it produced a kind of austere awe in the viewer. That happens with the daughter here, in an extreme and physical way. She's completely stunning: she's beautiful. She is also, however, deadly. This could be seen as the danger of the beautiful woman, or how deadly beauty can be, but I prefer the sublime.