I personally don't have a problem with the clay origin. It shows how a young girl (relative to the other Amazons) got on an island with no men, the piety of Hippolyta, and the benevolence of Aphrodite (and/or other gods depending on the version of the tale). About 4 billion people in the world today were taught that God created Adam from clay/dust and breathed life into it (not to mention a whole woman from a single rib). Also in some Greek myths, Prometheus created man from clay, with the breath of life coming from Athena. In Egypt it was Khnum who gave life, and in China it was Nuwa. It's not much different from Wonder Woman's creation myth.
Gods create humans from clay. It's part of the process. The clay forms are just vessels for the divine light/breath to fill. You could say Diana is closer to both earth and gods compared to other humans who have moved away from both through generations of reproduction. Part of her specialness is her innate connections to the divine, nature, and the "human world." Giving her a father didn't give her these connections; she already had them. Again, this is just on the idea of the clay origin, and not specifically about current stories.