Canon has been both the blessing and bane of Star Trek since the days of the original series. Interpreting it has almost become as intricate as legal debate or an argument before the Supreme Court. Precedents are set and canon becomes increasingly more flexible as time goes on...and even more often, convoluted.
I do, however, feel that there is a lot of creative room in canon in which to tell a very compelling Star Trek story without trampling needlessly.
However, the reality at the end of the day that trumps all this is the simple cold hard fact that Star Trek is ultimately a revenue generating multimedia property, and as such, the owner, to their benefit or detriment, can exploit it as they will.