I find the rumor hard to believe without more official confirmation. That being said, what am I supposed to do, just ignore the thread? So my thoughts are assuming it's true.
First off, tone would be a major issue. I have no doubt that Nolan would be capable of capturing the tone of each hero if he wanted to. However, the ideal tone he would capture isn't something entirely consistent with a single universe. This is especially true with Batman. He could have gone with a campier Batman tone (which has been done in the past), but the story would have suffered. I think Christian Bale as Batman makes far and away the most sense from a studio perspective for this movie (in fact, I wouldn't bother including Batman at all if it isn't Bale), but the necessary tone adjustment is difficult.
Second, the ending in TDKR doesn't have to be completely undercut. As long as the movie isn't set in Gotham, he can more or less "un-retire" to help out and then return to Italy after. Yes, he isn't technically free from Batman, but it's such a once in a lifetime emergency that it might make some sense. From a Gotham perspective, no one will really know it's the real Batman that did it. They can either play this big (scenes where he has to decide whether to help out) or small (he just shows up, maybe one scene where he figures out what's going on and decides to help). Maybe at the end, with the establishment of the Justice League, he knows that he isn't the only one who has to help out.
Third, since starting out with Superman would be stupid and I just made the argument why you can't start with Batman (although, from a story perspective, Batman would far and away make the most sense as a starting point since he is the most human and the most relatable), this means a different or new character should start. They have to make the Ryan Reynolds decision, but I'm not sure I would start with Green Lantern anyway since he has other logical people to turn to. That means starting with a different character and building a story around that character.