It doesn't have to veer from the T3 timeline if you believe that John would somehow forget or neglect to mention the fact he used to travel through time with a hot robot chick while being chased by terminators... Or think it makes sense that in the T3 timeline, he'd be completely surprised and caught unprepared by Skynet's continuing existence after the events we just saw in the pilot.
And while Sarah Connor could have traveled back to die in 1997, John specifically talks about her holding out just long enough to make sure Judgement Day didn't happen... which makes absolutely no sense for someone who time-traveled to 2007. I'm not saying she would have to believe that everything was hunky-dory just because the world was still there in 2007 - she'd simply know that the old date she learned about from Reese no longer meant anything.