The most important thing to note is that everyone has their part to play in this little charade. The Oracle's job is to identify the One and guide him to the Keymaker. The Keymaker guides the One to the Architect whose job is it to give him THE CHOICE. Once the (right) choice has been made, The One leaves the Matrix (along with a few hand-picked men and women from within the Matrix) the machines kill everyone in Zion and begin rebuilding it for the next generation to arrive. The One then spends a few years plodding around in the wilderness before "discovering" Zion and at some point over the next 100 years, the number of Zionese dissidents rises to an uncomfortable level and the cycle begins over again.
About ¾ of the way through his scripted conversation with Neo, the Architect discovers something odd. His little speech is expected to show the One the elegance of the solution and the forced choice he'll have to make. Bizarrely, Neo chooses wrong, stating that he is willing to accept the destruction of the Human race. The Architect attempts to dissuade him, but to no avail and Neo leaves.
Once Neo has made his choice, the Matrix is then living on borrowed time. Sometime in the very near future, there will simply have been too many intrusions and glitches that the average inhabitant will begin to question the truth of the Matrix. At that point, they'll start dying and the "crop" will be lost, forcing the machines to start over entirely. This isn't desirable, but it would seem that without a formal acceptance by a representative of the human race, it would appear that the machines aren't happy to keep the majority of humanity inside the Matrix against their will.
Architect: Failure to comply with this process will result in a cataclysmic
system crash killing everyone connected to the matrix, which coupled
with the extermination of Zion will ultimately result in the
extinction of the entire human race.
Neo: I don't believe you. And not only do I not believe you, but I've got better things to be doing.
Architect: What? Didn't you hear what I said. Everyone's going to die if you walk out of that door.
Neo: K thnx, bye.