Gordon's motivation is explained if you are paying attention. When Batman confronts him in the climax we learn about his Civil War experiences: the brutality of the war and the diseases spread by camp-followers and prostitutes. You might not find the explanation satisfying, but it's there. Now that I've watched the movie, I see that it is not so much an adaptation of Brian Augustyne's original story as it's a reinterpretation of it. Actually, I wish more elements of the original were still present, especially Jack the Ripper's previous activity in London of 1888. Of course then we would have to have had learned that James Gordon was also in London during the appropriate period. And eliminating 'Uncle Jake' from the film's story narrows our suspect pool for the Ripper, where keeping him in the narrative would have provided the audience with another red herring.