it reminds me of a science fiction book called Santiago... about a hero type robin hood character who the powers that be kept trying to kill... kicker was they did kill him... just that the person next to him his second, became the next santiago...
this could happen with john conner... the original keeps dying. the next person becomes john connor... even a sentient terminator could become john connor. till skynet is defeated. john connor must die... but can't. even if he does.
Have you been reading spoilers for Terminator Salvation?
The original ending of Terminator: Salvation would have seen John Connor replaced by a Terminator.