It does lend credence to the idea that this will be a three-movie arc:
Movie 1: Timeline changes; Vulcan destroyed
Movie 2: Earth falls "into darkness"; things go down with Klingons
Movie 3: Repercussions from 2; some grand resolution?
Maybe at the end of STID, the Enterprise will restart its engines in time to whiplash out of Earth orbit and time travel back to some period. I doubt they'd do a "Naked Time" rip, however. Too much time travel already (esp. if STID involves Khan -- not technically time travel, sure, but not a "contemporary" villain).