It kinda craps on the guilt Eccelston went through and that it was Rose who helped him heal, which has been a big theme throughout the RTD years
They're all supposed be the same man anyway.
I'm guessing that the last shot of the episode was going be something like the TARDIS appears and out step Eccleston and Piper. They would have always have been leaving that to shoot until they were making the Anniversary Special, so now it will be out step Hurt and Piper. So no longer a jump out your chair and cheer moment and more a WTF moment; less special but still a massive cliffhanger.