Here is one fundamental point about "rebooting" Star Trek in the manner they've chosen to do it. It makes all things possible and all things can still fit. I'm pretty sure nothing in this movie is going to rule out the primary events of any of the movies and to a slightly lesser degree, the TV shows. You may have to visualize some differences, but they're basic concept is that this movie's universe still ends up with one of those hundreds of Enterprise-D's in "Parallels".
I have seen the darkness in my soul and shine brighter for it.