Just a thought, unless your flight from Crete back to Athens is part of a common ticket back to the US, there is some risk in taking a budget flight from Crete to Athens, then catching a separately booked flight back to the US (Delays, cancellations, weather...) the same day.
You might consider splitting your time in Athens so that some is at the end of the trip, getting you there the day before your trip home. Not to mention, many flights to the US from Athens leave earlier in the morning.
As for Santorini, certainly something to see, if you are not planning on ever getting back, then maybe worth the cost and time. I would not feel bad about only spending a night, I did, saw many of the things I wanted, could have done more or could go back, but I wanted to see the view and Akrotiri, enjoyed a couple meals and I was fine.