I would disagree. Following your logic, we should now have "Wizard of Oz" as only the first silent film version (Sorry, Judy Garland and the gang), we would know only Lewis Wilson as Bruce Wayne/Batman (1943), and none of us would ever see "Hamlet" because the actor that first played that role died in the 1600s. J.J. Trek can coexist alongside Original Trek without causing an annihilating explosion in my universe. I am happy to see that TOS Trek is so successful that it merits continuation in film via a new incarnation.
As far as William Shatner goes- he does a great Kirk and a great Denny Crane and has sure had fun with the Priceline Negotiator, but I'd need to snort an awful lot of powdered tribble dung before I started thinking that Shatner was the greatest actor of all time.