Really not the case. At least not right now. Maybe in 2 months time when it's actually cold out. Right now, the air is as clean as it gets (not much but not smoggy either). It is only really bad if you're sitting in a car, in the middle of a traffic jam in the center of the city. If you're anywhere else it's normal for a 4,5 million resident city, if not a bit better.
The valley thing is true, the little air movement not so much. It gets pretty windy because Athens is built between two mountains and the valley inside gets narrow, fast moving streams. It occasionally gets no wind but most of the times there's a breeze. Not to mention the past 5-8 days, that I started to feel like we were constantly in the middle of a monsoon. The air was blowing so fast I could feel it driving down a very central 3 lane road here. You don't usually expect to feel the air pushing your car anywhere other than in a large highway.