Here's what I personally think. WB did in fact somewhat force Nolan into the ending we got in TDKR. And the whole thing about MoS not being a part of a future Justice League continuity is a total lie. They KNOW that they want a quick way to compete with The Avengers, so they're rushing through a plan to connect all these movies, with which Nolan's trilogy counts. ... indirectly. Joseph Gordon-Levitt (I'd put money on this) would be Batman in the Justice League film, which connects Nolan's trilogy to it. Henry Cavill is Superman in the Justice League movie. Bank on it.
The Dark Knight
The Dark Knight Rises
Man of Steel
(Whatever else is made; Wonder Woman, The Flash, etc.)
^^ They inhabit the same universe. You just watch. The easy excuse is that you can ignore everything outside of Nolan's trilogy if you want (which is fair). Bruce's story is done, Alfred is done - nobody really has to return except for Joseph Gordon-Levitt.