Thanks all for your input. We looking at mid-September so have a little more flexibility. If we end up deciding to go the flights route, we will book the following itinerary:

PAS 9:35AM > ATH 10:20AM
ATH 1:30PM > MLO 2:10PM

That gives us a 3 hour, 10 min layover, which we feel comfortable with and may even be able to stop by for lunch in the lounge