What if the purple ray was a portable device that channeled the quantum effects of quartz crystal?
'Knuth states that pieces of quartz were found in the 8,000-year-old Egyptian Temple of Hathor, and quotes the Greek priest Onomacritis, founder of the Hellenic mysteries, as giving the following advice in the fifth century B.C. "Who so goes into the temple with this in his hand may be quite sure of having his prayer granted, as the gods cannot withstand its power."'
So, when Themyscira was first founded, Aphrodite gifted the Amazons with a quarry of magical quartz, which they then learned to harness and direct the powers of, via technological innovation and extreme mental conditioning. A mix of science and mysticism that can be explained as the manipulation of quantum mechanics or worship/prayer to the goddess Aphrodite. It would actually be a combination of both. It could also give the Amazons various physical enhancements, such as enhanced speed, strength, stamina, and healing. I imagine them being built into their bracelets.
Think mother-boxes but crystalline (and therefore more ornamental in design).
1) Themyscira/Amazons Founded
2) Aphrodite Gifts Purple Quartz Quarry (Scientific Explanation: meteor hits island, showering in radioactive quartz)
3) Amazon Science-Priestess Develops Purple Ray
4) Kryskration/Cryscratium (lit. Ancient Greek for "Crystal Powers") Martial Arts
5) Amazons Incorporate Purple Ray/Kryskration Training into Culture
By the time Diana is born, all of the Amazons have enhanced strength, speed, stamina, healing, intellect, and senses. Amulets and other crystal-harnessing sources allow limited flight. Crystal-tipped arrows and crystal swords can cut through almost any metal known to man, and crystal armor generates a force-field capable of stopping bullets, etc.
The Crystals could also be used as a quantum gateway to other dimensions, allowing the Amazons to interact with "demons" and "ghosts" on the astral plane (but this is reserved for/sacred to the science-priestesses and the Queen).
I would actually have Diana invent the Purple Ray, make it something newly controlled that until her scientific mastery of the effects was almost completely mystical in its application (prayer, etc.). Or, hell, a new origin for Donna Troy could be that she's the teenage super-genius Amazon to invent the Purple Ray and acquire powers close to Diana's. That way the entire culture isn't flying around in the air, but they still use the crystals for magical rituals and the healing effects.
They can also be used to bend light around things, making them invisible = the Invisible Jet (make it Steve's original jet that crashed onto the Island).