A good idea, but I think it'd have to be pretty extraordinary circumstances for this to happen, something on the equivalent level the Norse Ragnarok. One of the common threads of Greek Mythology is that you can't escape destiny, and hubris comes from people thinking they're greater than gods. So, given that, and pardon the pun, I'd think there would need to be something to turn the spinners of destiny, the Fates, to turn against the gods. Perhaps Ares, wanting to create another divine war, conspires with the vengeful Hero to drive her husband insane or power mad, much like Cronus before him. Then Athena may have no choice but to strike down her father (bringing a level of Greek tragedy to the gods themselves). The Fates may then decree the age of the gods might be coming to a close with this divine war.
Of course, another angle to take is that the rationalism of the philosophers is beginning to displace some of the old gods (ala the Academy from Deities and Demigods). The world is beginning to be seen as more of a lawful, observable nature rather than simply a reflection of chaotic and moody gods. As his power wanes, Zeus becomes angry and jealous, much more controlling and stormy in disposition. As his wrath increases against mankind, Apollo convinces Athena to stand with humanity against a power-mad god. The Greek pantheon splits itself, but eventually Apollo and Athena win out. Athena wearily strikes down her father with a heavy heart, but then takes his place as leader of an (ideally) more rational pantheon.