How can something even be considered a choice when you don't get to see the results of that choice? What if the kid was completely lying? What if it was a stupid Matrix Reloaded type trick where everything you knew was just another form of control?
Speaking of that movie, what do you think the reaction would have been if the series ended after Neo walked through the door he chose? Certainly it would have spared us the further mediocrity of the next movie but I imagine a similar amount of head scratching would occur.