It still looks like both to me. He did kill them, but now he didn't. That's what time travel does.
Here's the thing that I think's key: the entire plotline is instigated from Hurt's time. A future Doctor isn't influencing him by coming back - he (or rather, The Moment) is actively seeking one out. It's reasonable to assume that The Moment would always do that, because at that stage in the storyline, there's no influence from a different time.
In your imagining of a situation where the War Doctor *did* kill the timelords, what do you imagine the Moment did in that situation? It's still the same Moment with the same conscience. Why didn't it prevent him there?