To those of you complaining that the End of Time’s ending no longer makes sense, I would like to point out that it, in fact, does. The above picture is a screenshot of the Master’s page in regards to the end of time. You can read the full page here: [x]
First things first, the Master and the Doctor destroyed a link between Earth and the then thought to be time-locked Gallifrey. A LINK. Not all of Gallifrey, as I’ve seen a few posts claiming. This sent them, and potentially the Master as well, “back into hell” of the final day of the Time War.
As far as the council knew, it WAS the final day of the time war. The council, as you might have noticed, was not in this episode. Probably specifically for this reason. They were too busy securing a safe escape for themselves through the White-Point Star. AND I QUOTE FROM THE EPISODE, “The High Council is in emergency session - they have plans of their own.” THIS LINE WAS VERY MUCH INTENTIONAL. In fact, the whole story line of the Master and the White-Point Star link could easily have gone down before the planet was stashed away by the doctors. In fact, that story line could run parallel to the Doctor trying to decide whether or not to destroy Gallifrey.
Now there are some saying, “BUT THE GUILT HE FELT WASN’T EVEN REAL.” No, it was real. As was stated in the episode, when they reentered their own time streams, the War Doctor and Ten individually forgot. And even if Eleven were to forget, Clara’s timeline was not changed, and therefore she would easily be able to remember and fill the Doctor in. It’s also why Eleven didn’t remember when he ran into Ten - because to his memory as Ten, it hadn’t happened to him. Getting back to the guilt, when the War Doctor (or 8.5 as some are calling him) woke up as nine, his planet would be gone. The last thing he would have remembered before crossing into the time streams would be trying to decide. His planet and all the Daleks are gone and only he remains, just as the Moment told him would be his fate if he chose to burn Gallifrey. And what can he find of his home? Nothing. So, naturally, he would assume that he chose to do it and that he killed his people, thus triggering the guilt in Russel T. Davies’ storyline.
TLDR: MOFFAT DID NOT IGNORE THE END OF TIME. PLEASE STOP.