I would go by your travel agent’s information and plan on the long slog. Not sure when your trip through IST is ( high-season? During Ramadan 3/23-4/21?) or how many are in your travel group, or if there are any mobility issues, but IST is a gigantic airport that involves a lot of walking with few moving sidewalks. The signage at the airport is sparse during the mile or more of walking that is involved. Worldwide, it is second only to the Dubai Airport in the number of international passengers passing through its terminal annually. That means you will need extra time to exit the secure area and re-enter through security to check in for the Athens flight. Be sure you adhere to all the rules for carry-on luggage or a delay may occur.
IST’s website says to arrive at the check-in counters 2 hours prior to your international flight’s departure time. It will take some time for your flight to taxi to the gate, passengers to disembark, make your way through the terminal to exit for the check-in counters after re-entering through security. As suggested above by Mister E, you might want to take a flight to ATH three hours or more after you arrive at IST to build in a buffer in case of any unpredictable delays.