I see your point about Athena, I she was the greek goddess of Wisdom/knowledge and war/strategy. However, you pointed out that she was the sister of Ares, which is very true, however, Ares - The god of war, is the Roman equivalent of Mars, which we've seen in The Magician.
I can see Dee or Nicholas go to Athena for help, however, she would probably help Flamel, because in the myths, Athena never liked Ares.
But with Ares, that would bring up Aphrodite, his girlfriend in the greek myths (AKA Venus). She could possible be... well enraged about happened to Mars
... But Aphrodite, as the goddess of Love, doesn't seem to have a place in this series... but she might later...
Also, since Flamel is trying to teach the twins the five magics, Earth, Wind, Water, Fire, Time, he would have to find someone to teach Sophie Earth, because she already has Wind, Fire, and Water (in The Sorceress). Could it be Gaia? (sorry about all the greeks, it's the mythology I know best).
And Josh would need to find those people too, only he need Earth, Wind, Fire, Time (not water...). He could go back to Saint Germain for Fire, Earth could be the same as Sophie, but what about Wind, I don't think the Witch of Endor can help there anymore...
Who's another goddess of wind/air/the sky...?