If they are a full member then I would agree that you should...but, it would be according to the earning rules for each individual FFP. Aegean currently has none defined. Most likely those agreements on earning rates haven't been completed yet. Once that is done you may, potentially, be able to retro-credit the flight. It is also possible that the earning rules, once introduced, will only be in effect from the moment that they are posted.

What you could do is open a support case with Aegean asking why there is no earning page for VL and against what percentage your flight will earn.