First of all, if you haven't been told yet, the Warnemuende Port is about 2.5 hours away from Berlin. It means that if you leave the ship for about 10 hours, you spend only five hours in Berlin. Even Szczecin is closer to Berlin, only two hours. This doesn't do Berlin any justice - it is a huge city with many sites from several periods, many world famous museums, and it takes several days to grasp it. So my first advice would be either to go to Berlin through Szczecin, stay there the night and return to Warnemuende the next day (if it possible with your cruise and its route); or to tour the area around Warnemuende.
However, if you're adamant that you'd want to go to Berlin:
(1) Be prepared NOT to see everything. I don't really understand what you're thinking of doing - it sounds pretty weird to me that a tour company does a "West Berlin" only tour, especially if you're in the city only for a few hours; or dividing the city at all. Are you planning to take one of the East (or West) tours and then try to do some of the Jewish sites on your own? I don't know if it is manageable, it all depends on your pace, on your priorities (if they leave free time, it is probably for seeing a museum), where they leave you and are going to meet your again (assuming that they are taking your to and from the ship), etc.
(2) Which brings me to the other point. It seem to me like you're locked on one tour company and I wonder why - Is it the most affordable? The one that the cruise company offers? Is it the one whose routes seem that most logical (or that mentions as many sites as possible on the itinerary)? In any case, I would shop around for more companies doing the cruise ship thing.