Of course, the other reason there are so few marinas in Greece is that there are large numbers of stone quaysides to moor up to free of charge!
It is also quite the exception to have smelly harbours. The only places I recall are Corfu town, Levkas, Patras town (not the marina), Pylos town (not the marina), Koroni, Gythion, a couple of places around the Athens coastline and Thessaloniki town. Everywhere else I've been I've had no second thoughts about swimming around the boat.