If you go back to "The End of Time" (I watched it a couple days ago), the High Council actually mentions specifically that the Doctor is still in possession of the Moment and could use it at any time. It was mentioned a full three years before we would find out what they were talking about. It was almost a throwaway line, and it's no wonder that most people don't remember them saying it. Everyone probably assumes that they're talking about the Tenth Doctor and whatever he was doing, but in reality, they were talking about the War Doctor. That's why they tried their little trick with leaving the time-lock, was to avoid the "burning" that the oracle saw when the Doctor used it. That plan failed.
Note that the time-lock mentioned in "The End of Time" is an intentional war measure done by the Time Lords themselves... that is NOT what was done at the end of "Day of the Doctor". Time still passes inside the time-lock, it's not passing where they are now. They're quite literally frozen.
So there's no conflict between the two episodes at all. In fact, they actually compliment each other quite nicely.
But it still leaves a lot of unfinished business. In "The End of Time", the Doctor mentions that the Time Lords had become more or less evil monsters during the war, and had to be stopped. That was why he was so intent to send them back into the time-lock, even though he knew it would result in their complete annihilation. If they ever find Gallifrey again, they're still going to have to deal with that, because the Time Lords won't have changed at all, and Rassilon will probably still be in charge of the High Council.
