It's good that Nolan was given the reigns over the DC universe.. he is a very good storyteller albeit with a totally different style than Whedon.
IF Nolan sets the JL (or any other DC hero) movies in the same universe as Dark Knight he has already set up events with the the end of Rises to have a believable successor to Bruce and tie in the movies to the greater universe.
Waynes' story is done and i would be extremely dissappointed in Nolan if he gives in to fan or studio pressure and has Bale reprise the role (as good as he was). A cameo or minor supporting role would be ok though.
Let's wait and see... Nolans' DC universe will be quite different in tone to Marvels' but that's a very good thing.