Watching End of Time again, it actually doesn't contradict the climax that much (in fact, they showed End of Time RIGHT AFTER the 50th Anniversary.) The 10th acknowledges Timelocks exist earlier in the episode, and we can assume he's tried to save Gallifrey before (in fact, in earlier episodes he's stated he tried and knows its impossible), and this is how he knows Gallifrey is Timelocked (despite the ending claim of "we forget this entirely.") End of Time doesn't actually say "Gallifrey is destroyed", just it's sent back into the Timelock. Now, however, the 11th knows how it got Timelocked, and thus possibly can find a way to break the lock later on.
Chances are it'll never be undone, granted, because that's kind of the hook of the new series (last Timelord, yada yada yada.) It works as an explanation given the massive elastic rules Doctor Who works on, or alternatively, "Time can be re-written" is kind of a consistently stated scenario, and the 10th openly states the oddity of the scenario in question and how something external must be letting them do it.
Oh, if we're counting specials like that, might as well mentioned I saw "Time and Space" special the night before, aka "Reinactment of the behind the scenes look to the William Hartnell Era of Doctor Who."
Dunno how much of that was real and how much of that was made up just to make the thing more interesting (obviously, even the real stuff would have some embellishment just to make it more interesting), though from what I understand it was a relatively accurate portrayal of how Hartnell actually felt in the situation. Guess it's kind of neat to see interpretation of what actually happened to get the show off the ground, and somehow I don't think William Hartnell saw Matt Smith, dressed as the 11th Doctor, as he was leaving the set for the last time...just a hunch <_<
