The Time of the Doctor special gives the strong impression that the future has been changed. The Doctor does not die at Trenzalore. The planet does not become the horrifically scared and burnt graveyard depicted in the Name of the Doctor.
The events that transpire in the Time of the Doctor do make clear that the destruction of Trenzalore was a possible future, but is not the future that eventuates.
Does this mean that the events of the Name of the Doctor are to be considered an aborted timeline? And what of the Great Intelligence? Does he therefore still represent a dangerous threat to the Doctor? And how are we to view Clara's courageous acts to counter the G.I.? Perhaps her splintering across time never really happens. But then how can the Doctor's earlier encounters with her be explained?