Have you considered just flying to Santorini from ATH? It seems like such a waste of time to schlepp all the way from the airport to the port when you could wake up leisurely and be in Santorini in 20 minutes.

On the return, I would stay downtown. That way you can go back to the hotel after a day of sightseeing, freshen up, and go back out for dinner. Traffic in the morning for the airport won't be bad at all.