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On second thought, I completely agree with your analysis except on one point.

I think that the architect conceeded that choice was an inherent natural property of humanity. Hence, in the end, Neo must choose whether to redo the matrix or go back to save Trinity. It is his choice, no matter how much his emotions may drive him.

(This is, of course, predicated on the fact that the architect isn't lying. The oracle was because she needed to trick Neo into making the choices she wanted...should make for an interesting third movie)

The matrix guides us into making decisions. If we accept that Zion is another level to the matrix then the accident on the hovership that caused Trinity to have to go back in is a part of that guiding that the architect does. However yes. You eventually get to a point where choice can not be guided or at least entirely predicted.

As I heard someone say, it's like Deep Blue. It can predict every move you'll make and guide you into making certain decisions so you'll be where he wants you to be 10 moves down the way. However there's always that chance that you'll break behavior or you'll not choose as he predicted then he'll have to alter the playing strategy to get you into following his prediction.

Neo's choice at the end of Reloaded IMHO was not predicted by the Architect. He probably expected Neo to choose to save humanity. As a result the resistance would have been wiped out and it all could have begun again.

As he said....it all comes down to choice.