For the "origin" of the crew there was very little continuity to worry about. The books and spin-offs are not even a consideration. At best they had maybe 2 - 3 episodes that had vague references so it was pretty wide open to do without having to CHANGE the characters completely. This is the biggest problem I had. It was lazy writing with cheap shock values thrown in. It's interesting to note that (I hate to do a Star Wars comparison but...) when Lucas changed Han Solo to not fire first, everybody was in an uproar because it IMPLIED a change in character. In Abrams' movie they explicitly change the characters completely(with the exception of Bones who was closest to the original) and the majority are ok with it. They have set precedent. The "prime universe" is now in the past and over-written. For all intents and purposes, this new "timeline" in the new prime universe and everything that follows will be based and referenced on that.