What about Thor and Hercules, they were in the Avengers. Wonder Woman is also tied into Mythology in her Origin. The Golden Age Flash's looks were based on the Roman god Mercury (his helmet and the wings on his shoes).
So the connection is not that far off, but it is however a very superficial one, as you say.
Marvel's Thor has very little to do with the one from the Myths.
Alan Moore poked fun at this with his great 1963 series by giving Horus a marvel style make over:
http://www.comics.org/coverview.lasso?id=53442&zoom=4So whether or not you get that Grant Morrison was being ironic or believe nah, he is just an idiot who does not get it, depends on your own opinions going in before reading his comics.