If you are not sure for the reason of the delay (it seems ATC, not necessarily related to GOA departure, might be enroute), I suggest you follow the procedure in these cases:
* Submit your claim to the airline and they will get back to you. If they refuse EU261 compensation they will tell you the reason.
* As another step (i/o the online compensation firms), you can also submit a complaint with the relevant authorities (Italian and Greek) since they can investigate and fine the company if found not following the regulation. In that case the airline will most likely get back to you with the compensation since the fines are much higher.
Good luck!