I think it's more to fair say that the Greek myths in general were rather misogynistic, and also that many of the gods and goddesses are more akin to forces and themes than simply good or bad. To take some exemples, Demeter is both famine and a bountiful harvest; Poseidon is the sea in all aspects; Apollo is both sickness and cure. They do not conform to the modern view of gods as beings of ethics at all.
And yes, I agree that any feminist (because feminism in some form is the core of Wonder Woman) take on the Greek mythology is likely to run into the problem of goddesses good; gods bad. It's a problem I struggled myself in the old Revisiting Olympus thread.