If the original *ticket* had actually been ZRH-ATH-HER and Aegean had still gone the same about solving the issue, then yes, I'd totally agree with your view on this (and, like you mentioned) there would also be compensation involved.
I would also be willing to bet my right hand, that Aegean would have either put the passenger on the direct flight or suggested a different, more "direct" solution.

However, that was not the ticket that was issued (it might be a bit hard to understand, depending on what your point of view is, but that's just the simple truth). It is more of a technicality in its core, but it certainly does pose practical issues for Aegean's (and the airport's) employees (in short: the way it was originally ticketed, the "pass" being a major factor here, most likely left them without any other options).

It might help with your perspective into this if you compare what it looks like (also €€-wise) to book a ZRH-ATH on a pass and then a regular ATH-HER, to booking both ZRH-ATH and ATH-HER without a pass (but still separately) to booking ZRH-ATH-HER together in a single booking (or any similar combination of a pass destination/origin and connecting flights).