Hmm. Maybe you didn't understand the plot as well as you think you did.
You mean reducing TOS/TNG/DS9/VOY and movies I - X to one of the infinite universes where "all possibilities that can happen, do happen, in alternate quantum realities" (along with the timelines where Worf married Troi, the one where everyone's evil and the one where bunnies rule the universe)? They put the whole timeline
on a bus.
Nothing to do with timelines. They jumped realities, not timelines. Or maybe they created a new timeline, which is the same as creating a new reality. The usual reset-button scheme wasn't followed in XI, that's for sure.
Whether or not this is part of the multiverse idea is very much open to question. We know about three realities so far - Prime, Abrams, Mirror - maybe there are only those three, and everything else is all about futzing with (and improbably repairing) the timelines within one of those three.
Personally, I find the idea of the cosmos stopping at just three realities to be ludicrous. Why not four or five or five quadrillion? Why stop at any particular point on the road to infinity?
And if the number of realities is infinite, that explains how you can "repair a timeline," which sounds flat-out impossible to me. It's like unscrambling an egg. They aren't unscrambling the scrambled egg, they're finding a new egg and declaring it to be the same one as the one that got scrambled. Sure, there are some differences, but an egg is an egg, why be fussy?
But what's true for the natural world doesn't need to necessarily apply to fiction. Also, it is upsetting to think about all those eggs, cruelly abandoned after being scrambled. Three it is.
And as a final thought, the statement about the timeline "trying" to repair itself does make me think the idea here is that the timeline will end up looking like the Grapevine on Interstate 5 - it splits at a certain point, and then re-merges later on. So by the time TNG rolls around, the timeline could be totally repaired and ready for action.