I've no specific experience of OA-TK but I have had them do some pretty 'non-standard' through-checking in the past (Malev, Emirates) as well as many *A members so I think you will be fine. The staff at the small island airpors tend to be pretty helpful and flexible in my experience. Do let us know.

As for the Athens transit - even if you are through checked, you will still have to go upstairs (there is a transfer escalator just after you enter the terminal from the bus), make your way from the B to the A gates (a two minute walk) and then pass through immigration then security. There is no airside transit. ATH is a pretty efficient airport so, as Klouis said, you should have plenty of time either way, but be warned that the Swissport lounge in the A gate area is pretty bad, so don't be too worried if you don't find time for a visit.