Sounds like it might have been cool, but I like that there are 2 separate time lines, rather than 1 trying to fix itself. Or am I no understanding what Spoke Prime was saying?
I think you're understanding it, and I think the line was cut because, no matter how they tried to write it, it hinted too much at a single timeline instead of the two separate ones they were trying to get across.
From this TrekMovie interview
(published April 30):
TrekMovie: Even though things are different in this timeline, like Kirk coming aboard the Enterprise first as a cadet, by the end of the movie every one of the original bridge crew end up where they are supposed to be. Is there some kind of notion that it is their destiny to be on that bridge, regardless of what timeline you are on?
Kurtzman: Yes. In fact there was one version of the script where Kirk points out that it is incredibly odd that they all sort of turned as they would have. Nimoy Spock tells Kirk ‘I knew this character as this person and that character as that person’ and Kirk says ‘wow, those characters are exactly the same ones that I know’ and Spock says something like ‘Fascinating, that must be the timestream’s way of trying to mend itself.’
Orci: It is a nod to destiny. And there is still something like that in the film.
, TrekWeb has excerpts from the Star Trek Magazine interview, which contains this, from Kurtzman:
AK: It's funny you ask about time travel and the idea that time sorts itself out. There was a line that we had written that was shot which ended up getting cut from the movie. Watching it the other day, I wish we'd kept. When Kirk and Spock Prime are in the cave and Spock's telling him everything, there's a mention by Kirk of "How is it that I found you in this cave in the middle of an ice planet? It's insane that we should ever even meet this way." Spock says, "Perhaps it's the timestream's way of trying to mend itself. It is fate and destiny trying to bring us together."
Looks like I misremembered about who said they wished they'd kept the line in, and he says here that it was
filmed but not used. Maybe it didn't end up in the extras because it wasn't an entire deleted scene?