Probably the most common version of Medusa's monstrous transformation claims that she was raped by Poseidon in Athena's temple, and as punishment for the sexual act in a temple of a Virgin Goddess, Athena turned her into a hideous, killer gorgon with snakes for hair. She then lived a life of sheer terror toward the human race, turning every human being into stone with a mere glance of her condemned eyes. Borrowing Athena's shield to protect Him, the Hero Perseus later killed Medusa. Her stare was so powerful and eternal that her reflection was burned onto the shield of Athena as it protected Perseus, and has remained ingrained upon it ever since.
It's important to remember that there is more than one version about how Medusa came to be the ill-fated creature of her final days. The idea that she was punished for being raped mainly comes from the poet Ovid, who was Roman, not Greek. In other versions, probably more Greek as it seems that Hesiod goes in this direction, Medusa was actually born a gorgon monster naturally and thus was not punished at all by any God for anything in terms of being turned into a monster. She was simply a chaotic being who obviously, in the end, needed to be disposed of for one reason or another. (Source)
Those of us who are Hellenic practitioners would most certainly dismiss the rape theory, as we know that we can discredit it with Hellenic theology itself. We know that our greatest philosophers thought the Gods to be all good beings and that they do not participate in anything evil or unjust, such as a brutal rape and also punishment for it upon the unwilling victim. These actions are not within the characters of Gods. If the actual Medusa was indeed sexually assaulted in Athena's temple, or in any religious sanctuary, my bet is that it was an unidentified assailant and there was no other way to explain why this could happen in a temple of a God other than to blame it on another God. In this case, Athena's greatest mythological rival (Poseidon) would fit the placeholder for the myth.
In the Goodness of the Gods,