We have a 7 AM outbound flight from Catania before the airport car rental opens. Do they do drop boxes like in the States?
Have you asked your rental car provider what provision they have for off hours drop off?
I am sure they hang a drop off box but definitely a question for the rental office. If you are renting from the same location it would be a easier since you can be shown exactly what to do when you come back after hours.
Never dropped off after hours in Italy but did so in Norway similar situation as yours, small airport and it was really easy.
There was a drop off lot, parked went inside the terminal where the rental booth is and they had a slot for keys to be returned.
I would most definitely get the full insurance on that rental as you will have no way to disprove damages if no one checks you in.