The naruto that talked to itachi couldn't be a clone for the fact that if sasuke could tell which naruto was real in his fight with him i would expect itachi to do the same, and i also remember him thinking to himself on wheter he should run or not.
The ability itachi inplanted in naruto wont be a move to kill sasuke in a last ditch effort for the fact that he pretty much asked naruto if there was a chance that he would kill sasuke would he? i think he asked him to see wether or not he would kill sasuke which he doesn't want and to be assured that naruto would try to stop him from destroying the village. him saying lets hope you won't need it means lets hope sasuke doesn't decide to attack the village.