Nah, there's no way they would have killed Gordon, especially before he was made Police Commissioner; he's too much a part of the Batman lore/mythos. That's a flaw the Burton/Shumacher films had: an under use of Gordon.
True, but we knew Nolan was only going to be making 2 or 3 of these movies, and then the story would most likely be rebooted yet again with a new style and director. So why NOT do something really big and shocking, and shake things up?
(Of course I also think the movie wimped out by not having the people on the ferry blow themselves up, so maybe I just have a weakness for really dark and tragic endings. lol)