Hell, I'll bet that they did the whole "alternate timeline" thing for the sole purpose of letting the fans know that they can go to sleep at night with the knowledge that their favorite universe is still intact somewhere. I'm fine with Amanda being dead, I'm fine with Vulcan being gone, i'm fine with two Spocks, and I would be ok if there was more major changes in the next movie. I nominate the Russian wizz-kid, Ensign Chirpov (
) for the next casualty.
Except that they didn't do the whole "alternate reality" thing, they did indeed do an "alternate timeline" thing, aka, the old timeline is gone, destroyed, changed, now the alternate timeline exists; as all time travel stories in Star Trek did before. This is what Spock described - a changed timeline, the old one being gone and destroyed.
Uhura then just pulls the term "alternate reality" out of her ass that has nothing to do with anything that Spock just said, and for some reason Spock just agrees with her.