I don't know if other pass holders have had other experiences in similar (and I do want to stress "similar") cases, but I personally don't see anything "wise" or "logical" about changing a very restrictive pass ticket to a "regular" ticket on a totally different route. I am pretty sure there is no way to do this other than to cancel/change the pass ticket and simply purchase a whole new ticket for the other flight, which I would presume would have been at least as expensive as what Aegean paid for their good will gesture (which they will make more often than not if not nearly every time, even when on different tickets trying to "connect" two flights, well, at least the accommodation part, not the whole "free upgrade" part) and I will also assume that Aegean (or at least the employees at the airport) wouldn't just issue him a "free" ticket for that flight.

I personally don't find what they did illogical (though certainly very customer-friendly), but I do understand why it could be considered to be the least effective solution.