They could have let Nolan do ALL of that stuff. In fact, theoretically, the movies could have been EXACTLY the same. You just need a tv miniseries or something that shows that, without Bruce Wayne, Gotham goes down hard to crime...and set up the need for Bruce to return in another movie. Or they could have just dictated to Nolan that, while he would have total creative control, he would not be allowed to permanently remove Bruce Wayne from being Batman.
DC Comics reboots fairly often...but in general when a writer exits Batman, they keep building off of what they wrote...and the new writers tend to be aware that Bruce Wayne will at some point have to be the focal point of the long-term Batman franchise.