I don't think that's an accurate interpretation for the scene. It wasn't that the timelines didn't diverse - just by having someone enter the past creates a timeline with differences, it was that the Ancient One's new timeline would be defenseless without the Infinity Stones.
As a side note, a lot of people have interpreted this broadly (the Infinity Stones preserve the timeline). I think it's simpler. She could see the future and knew the Time Stone was needed to protect from Dormammu. I don't interpret her as speaking for more than the Eye of Agomotto. Ultimately, I suppose, it doesn't matter either way.