I have mentioned several times by now here, that Aegean's call center is full of people, who have no idea in some matters, because they themselves have zero actual, practical experience with many issues. I still find it somewhat unexpected, that two agents would "assume" (because that's what they always do, when they either don't know, or they think they know), that you initially "flex" purchased ticket would allow you to take advantage of business class cancellation policies. Which if you ask me would be completely logical (since eventually you did pay the entire price for that business class fare, unfortunately that's not how it works), however I too only know about this, because I had to go through the same process once myself and find out the hard way (though I did have an agent actually let me know what the outcome would be in the last second, so I rebooked instead of cancelling).

What I think you could have done by phone in this case is to request re-routing (without cancelling). I've also done that without irrops being a reason and Aegean did at with minimum cost for me.

For now I'd second ariadgr's suggestion, maybe this will grant you some exception to the rule.