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.
I'VE come to accept the new timeline as wholly separate in most respects from the old, classic and well-trodden one. I guess in the TREK universe they might be the same in some quantum respects but for the sake of the audience's sanity and even many Trekkers' we should just consider this movie the start of a new and uncorrected timeline that skewed BACK TO THE FUTURE II-style from the original one and exists in its own right.