welcome to Cruise-Chat.com. I have moved your question to the Europe Port Chat forum, as it is a port-related question.
Indeed, it's a long journey from Warnemünde to Berlin and unless you see this as your only chance to ever visit the German capital, I would suggest not to take the excursion. It is simply not possible to get more than a very tiny glimpse of Berlin in just a few hours.
In Warnemünde, the pier is only a handful of yards from the train station with regular trains to central Rostock (Warnemünde is a suburb of Rostock), which has a nice city center with historic places. Also, Warnemünde itself is a beautiful and virtually unspoiled seaside resort, perfect for strolling on a nice day. Of course you will have to try some German food (and probably beer). Everything is within a very short walking distance from the pier in Warnemünde.