Yes... online it says you are there from just 8:00 am to 2:30 pm. And you are right that you have to tender.
One way to assure you get off earlier is to sign up for a tour, as they take those people first.
The other option is to just to be among the first people in line to get a tender ticket.
Also (a little secret, don't tell) - unless it is very packed there are often spaces on tenders. If you just sort of meander down to the loading platform you may be able to squeeze on - but I didn't say this).
Finally - I wouldn't think it would take you taht long to get off the ship, especially if you arrive early for a ticket. But if it does then I assume you don't have a tour planned - which means all you want to do is see Thira. Three hours is probably plenty of time to see it. In Thira definitely go to see the local Museum. It has all the major artifacts from the island including the original painting of the two fishermen.
If you want to see Akirotiki then you should get on a tour in my opinion, since you will want a guide anyway.