Is this on one ticket or two?

If two tickets Aegean would not have to rebook you. You may be eligible for compensation if you were notified (and/or found out and talked to them about it..) within 14 days of departure, depending what the final delay was arriving into GVA. Though that doesn't help you much if that causes you to lose the long haul flight.
You could consider asking for a refund for the Aegean flight; and booking any other carrier that has availability.

If all on one ticket, then this really is an Aegean problem. You could consider just taking the flights, and if you do miss the connection in GVA because you have to re-check luggage there, then that is on Aegean to resolve. Meaning to rebook you, and pay compensation for the full itinerary.