Bloop.

Athena’s hands were tied. Yes, she was a powerful Goddess, but she was very much a woman in a “boys club”, and the true offending party (don’t think for a moment that Athena blamed Medusa for being raped in the temple, Athena knows better) held all the cards. There was nothing that Athena could do to punish the true criminal, and she was expected to punish Medusa by everyone else. What’s a Goddess to do when she cannot punish those who need to be punished and is expected to punish not only the truly innocent party, but her most beloved follower? Use that incredible brain power she had to protect Medusa at all costs, and of course the men would see it as punishment, to be have her beauty stripped from her and sent to live in the shadows. Medusa should have been KILLED for supposedly defiling the temple, whether she truly did or not, but she was given the gift of life, and the ability to protect herself and her daughters (who she bore thanks to Poseidon). This is why Medusa’s image was used to signify woman’s shelters and safe houses.