The episode shows how avoiding war can be difficult but worth it. It was obviously an easier solution in the practical sense to just destroy both sides to end the war. However, easier doesn't mean better. In the end, the Doctor found a better solution using his creativity and ingenuity. That is thoroughly a Doctor Who theme and perfect for the anniversary special.
Agreed. Plus it's not like it was just some casual or arbitrary decision on the Doctor's part to change history. It still took three regenerations and hundred of years of agonizing over his prior decision before the Doctor was able to come up with this new solution.
And it required a Doctor as nutty and off the wall as the Eleventh to think of it as well (who had a Companion like Clara who would inspire him to try something different, and more in keeping with who he is).
So I don't see this as Moffat "undoing" the effects of the Time War at all. This is just the natural progression of the story, with the Doctor doing what he does best and coming up with a new and completely different way to approach the problem and save the day.