It's always been a case of the doctor trapping the entire war in a time lock. One of the key aspects in Moffat's run is that the doctor keeps changing things but on the surface level, it remains the same (e.g. he died on lake silencio as far as anyone is concerned, and he was there, but only inside the tesselecta-something)

I think right now things are status quo at the surface level:

1. people assume that the daleks and the timelords were both wiped out by the doctor
2. the doctors (post-John Hurt and pre-Smith) are still guilty over wiping out the timelords
3. Surviving daleks believe that the doctor wiped them and the timelords out at the same time with some kind of weapon (instead of their crossfire)

...even though the timelords are perfectly fine somewhere out there.

What I don't get about the whole timelock thing is why the doctor is so guilty and why it's referred to as a genocide or a massacre of an entire civilization, even though the series (Tennant's last special and the one where Jack Harkness trapped Torchwood inside one) has already shown what happens inside a timelock and it doesn't look that bad, especially since there's an entire planet inside the timelock.