Another reason Athena may have punished Medusa is that she could not punish Poseidon. Athena, while a very influential goddess in Greek mythology, is outranked by Poseidon in terms of status. If Athena were to hold Poseidon accountable for his transgressions against her, the goddess' father, Zeus, would have to punish him.  The situation becomes trickier since Poseidon is also Athena's uncle (Zeus' brother). In a case like this, Poseidon would arguably garner more favor with Zeus as opposed to Medusa. In these kinds of disputes, the gods tended to have the upper hand as opposed to mortals as well, which also probably contributed towards Athena's verdict.  In turn, the only way for Athena to punish Poseidon is by punishing Medusa. Athena knew that Poseidon lusted after Medusa, this was made evident by his ravishing her. So to get back at him, Athena cursed Medusa so that Poseidon couldn't seduce him anymore.  One can argue that Medusa is caught in the middle of a crossfire between two deities. Due to her involvement in their feud, Medusa likely suffered a punishment that was not explicitly intended for her.
Despite Poseidon outranking Athena within the Olympian hierarchy, that has not stopped her from challenging the rival god before. Both gods desired to be the patron deity of Athens, so much so that they almost went to war with one another. They would eventually settle this dispute with a contest between the two gods to decide who would become the patron of Athens.  If there were an imbalance between Poseidon and Athena, then Poseidon would have claimed Athens as his city regardless of what Athena wanted.
Rejecting the premises