JJ is either a genius for throwing out 40 plus years of trek and Starting over or a moron.
Canon in such big fictional Franchises needs to be able to expand and contract. A lot has been added to the canon throughout the years. Similar to Star Wars it is almost impossible to make everything match up without Contradictions and so forth. In Lucas case he very wisely set the EU apart from the films to avoid having constant retcons. Yet he went ahead and did worse to the canon than the EU ever did with the prequels and Special Editions continued to be tinkered with to fit his current vision of his created universe.
The prequels and their canon was so vastly different from the Original Trilogy i sometimes wonder why he did not make them to Match the original films or completely Remake the old Trilogy. At least in that scenario the originals would be untouched and would not have to be buried.
Kirk as a rebel was started by Nicholas Meyer and Harve Benett. Star Trek II revamped the series and injected Shakespeare drama and classic literature, as well as militarism that was not a part of Roddenberry original design at least according to him.
I personally don't think Star Trek was always that way. His philosophical outlook changed during the Movie years and during the Next Generation. His vision of the future could no longer have conflict. Everyone worked together, and there was no disease, hunger or money. Star Trek did originally have social issues Talked about in the guise of science fiction and a quasi hippie idealism to it in the begiinning. But it also had conflict and Was basically a space western.
There was sex and violence at least what was allowed in those times in the rejected "too cerebral pilot" The Cage.
Roddenberry like Lucas after him took way more credit than was his due by Appropriating the work of his employees and claiming it as his own. A great deal Of Star Trek was Dorothy (D.C.) Fontana and Gene Coon. Also Samuel Peoples. Nimoy himself pretty much created the character of Spock with Little to go on from Gene's rough idea. Just like the Kirk character was Created and interpreted by William Shatner in a way that made the character live and breathe. Actors are a large portion of the creation and they almost never get the recognition they deserve especially in science fiction.
Mark Hamill, Carrie Fisher and Harrison Ford should be applauded for breathing Life into the characters in the original star wars trilogy. Had the characters been played by Hayden Christensen, Natalie Portman etc. they would have been as sterile as the prequels and its phony cgi are.