I think people are forgetting that Bruce Wayne is one of the smartest human beings on the planet (up there with Luthor and a few others). I am pretty sure he is more than capable and has the intellectual know-how to pretty much get anything done, including getting from the Middle East back to Gotham in a short amount of time. He isn't just a human being only capable of ordinary feats.
In Batman Begins we saw him travel throughout the world without using any of his family resources. This is also before he trained with the League of Shadows, and became Batman. Since that time he has only grew his knowledge and his wisdom, so obviously he is even more capable than in Begins.
I agree that there should have been a scene of him finding a way back into Gotham, but the movie was already pushing 3 hours, so maybe it was cut due to time constraints? But, even considering all that I firmly believe Bruce Wayne of all the people in the world would have no problem finding a way back into Gotham. He probably has many secret entrances built in throughout the city knowing they may be useful some day.
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