Let me get this straight, you think a bumpy approach is somehow down to an earthquake on the ground ? Or was all this bumping and shaking occurring after all the tires were firmly the tarmac ? In the case of the latter, you may well be onto something... in the case of the former, I'm not quite sure I follow your reasoning as to how an earthquake can affect an aircraft in flight.
Given the destination of your flight (Greece in the summer), more likely to be strong thermals from the ground caused by the heat.
As for some sort of minor flexing in the wings, watch this video and rest assured wings can put up with a lot more than they'll ever see in their lifetime...