I've never been a fan of this destiny business in the film. I'm happy the line was omitted.
Neither am I, but it would have been preferable to the old band of the TOS crew showing up on the Enterprise by a series of incredibly staggering coincidences. Suggesting that's the timeline working mysteriously to heal parts of itself would at least be acknowledging the nature of the coincidences in an effort, however half-hearted, to explain them.
Oh well. When I first watched the film I got no impression there were two timelines anyway, to be honest - it's worded carefully so that interpretation might be drawn from it (as O&K insist) or it could just be seen as time being rewritten again.