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It is not stupid because I do not understand the problem, it is stupid because you think “avoiding cisnormativity” is more important than an accurate translation. When characters address Athena in disguise, they are not addressing Athena, they are addressing the disguised Athena. If she is disguised male, of course they address her as male. However, when Athena is mentioned as Athena, she is female even if she is in a male body because Athena is female regardless of her disguise, just like Zues is male regardless of his disguise. You are projecting your own modern assumptions into a historical text that did not have any such assumptions.

This is kinda stupid. When Zeus comes down as a swan or a bull, does anyone change pronouns to it?