The only problem with Rome is there's way too much to see! A good problem to have, but in the limited time you have on a one day visit, you definitely want to make the most of it.
That's why I agree with Pete. Much wiser to book an independant private tour, particularly if you want to do a Vatican tour.
Try and find another couple or two to bring down the costs, but do it regardless.
The crowds for tours of the Vatican are crazy most days. A good guide will pre-book your tour, and you'll walk right past blocks long lines to get in.
Whether with a private guide or a ship's tour the place is so crowded, the pace once inside is guided by the movement of the crowds.
After the Vatican tour, the cruise line tours eat a lot of time with a long stop for lunch. And lunch with a large group does take time; as does gathering up stragglers.
On a private tour you can get a good quick bite somewhere, and still have time for many more highlight sites, before heading back to the ship.