I haven't seen the movie yet, but your comment and a couple others leave out something important: 2009 was a reboot of the post-USS Kelvin era. In other words, since Khan came to power in the late 20th century, the Botany Bay should still have flown off into nowhere (1996, wasn't it?), and he and his crew should still have gone into hibernation. Why would the events of 2009 cause any significant effect on someone who is fast asleep somewhere on the other side of the quadrant? That's like saying the Borg shouldn't exist now.
What it does give the movie moguls a chance to do is rewrite all of the stories we're already familiar with, and/or take them in new, maybe weird directions - but without necessarily eliminating the characters those stories were written around. We already know that Pike doesn't end up a vegetable anymore, let alone ending up on Talos IV. By the same token, maybe the Doomsday Machine (which originated outside the Milky Way) will "decide" to take a turn somewhere that it wouldn't have, owing to the absence of Vulcan. Or maybe the Enterprise won't show up at Janus VI and the Horta will go extinct at the hands of the miners there. There are tons of ways to re-use the characters and events of TOS and beyond.