Before peoples' heads spin, hear me out. If the rumors had been true & the Amazon in the Man of Steel sequle were indeed Kryptonian, I have come up with a logistical way it could work & not really change any of Diana or the Amazons' origins.
Thousands of years ago a Kryptonian scout shuttle, Olympus, crashed into the side of a great mountain in ancient Greece. Due to our atmosphere being hostile to the Kryptonians, they stayed inside the ship for many years; however, because of the effects of the yellow sun on the Kryptonians and the outside atmosphere leaking into the ship, over time they assimilated to our environment as well as developed godlike powers. While the Kryptonians where still inside the ship, the primitive natives begin to colonize at the foot of the mountain creating great myths of what was inside, stories of powerful Titans. These primitive villages were the early stages of what would become a great civilization. As the Kryptonians began to emerge from the ship, the primitives mistook them for Gods; children of the Titans they had imagined were inside, thus the birth of the Greek Pantheon. The first to make himself known to the humans was Zeus, the super egotistical leader of the crew with a overzealous libido. Zeus fathered several children with the natives, each with great powers elevating them above humans. Over time, the ‘Gods’ became more curious about our kind and begin to study us, their machinations guiding the Greeks as a race. Due to Zeus’s infidelity, his wife Hera gathered other ‘Goddesses’ and create a watery gestation chamber, the Gia, located off the coast of Greece and there they spliced their own DNA with the bodies of slain females, creating a hybrid race; half human, half Kryptonian. Believing they would be more peaceful without cheating husbands, the race is all female and because the yellow sun extends the Kryptonians’ life to near immortality, there is no need for males to mate with. The first to rise from the water is called Hippolyta and in time becomes the queen. Several of the female ‘Gods’ care for and raise their new race of Kryptonian/ Human hybrid females and in time they come to be known as Amazons. The Amazons, being half Kryptonian lived much longer than humans & have greater strength; however, due to their hybrid DNA and originating from Earth, the Amazons do not have a weakness to Kryptonite. Above the gestation chamber, the ‘Goddesses’ create an island home for the Amazons, hidden from all others and restricted from the violation of males. To protect the gestation chamber, the Amazons are told it is a great evil and they are bound to protect and guard it. As they grow, the ‘Gods’ train them in many of their ways, including warfare & science. Over time, the human side of Queen Hippolyta began to cause her to yearn for a child, unknown to both her & the “Goddesses’ who created her, Hippolyta was pregnant when she was slain and the essence of the unborn child was still inside her. Zeus, who had admired Hippolyta from afar and unable to control his urges, appears to the queen of the Amazons and they began an affair. The result of this affair was a daughter, Diana. To hide the true lineage of Diana from Hera, Zeus and Hippolyta fabricate a story that Diana was created from clay & granted life by the ‘Gods’. Since Diana is 2/3 Kryptonian, she is stronger than other Amazons and can fly; however, like the other Amazons, she is also immune to Kryptonite.