ATH is a very efficient airport, and I'd expect to transit it in comfortably less than an hour - in fact, more like 20 minutes on an extra-Schengen to extra-Schengen itinerary as yours is. Your route will be arrivals area-immigration-gate area. There's no need to collect your bags, and you'll depart from the A gates.

Of course, the minimum connection time will be set much longer so a protected single ticket will reflect that.

Europe does not operate a standby system, so you should expect to travel on the booked flight over to Larnaca.