I mean, how bad do things have to be before you bring someone back from the grave to be your totalitarian dictator? I'm guessing pretty bad, and I'm guessing at that point you're fighting back pretty viciously yourself, even if the Daleks started out as the aggressors. But this episode completely bypassed any of the moral questions of who's the bad guy here, choosing instead to make the Time Lords out to be bumbling and innocent, and ignoring the fact that genocide, even of an evil race like the Daleks, isn't something to wholeheartedly celebrate--a lesson the Doctor has come face to face with TWICE before the Time War, but which Moffat chose to forget.

I agree very much with this! As things stood before, the Time War showed us that war tends to draw even the side that started out "in the right" towards evil, and the ultimate endpoint was MUTUAL destruction. No one won, because war has no true winners, just damaged survivors. In contrast, The Day of the Doctor essentially tells us that genocide is an acceptable and expeditious path to victory. Even when the opposing side is the Daleks, I don't think that is a good message. As you point out, the Doctor has in the past refused to exterminate the Daleks. Here, I don't recall the slightest hint of conflicted feelings about it.

While I never loved The End of Time, I think it's cool that you (with your superior Classic Who knowledge) found that it led to interesting headcanons about what happened to bring Gallifrey to that point!