When the Architect asked Neo to make his choice one of the TV screens revealed that Trinity had been shot by the agent. However, the movie indicated that she was shot after Neo opened the door on his left. Didn't the Oracle say he can't see past any choice?
I think the Architect already knew in advance when and how Trinity would be shot. By reading Neo's chemical precursors in the form of code, he probably also knew in advance which door Neo would choose to open. Why bother asking Neo to make his choice if the Architect already knew Neo's choice?
Since the Architect knew Neo's attachment to Trinity, it seemed unwise to endanger her life. I think that even if he's not interested in studying irrational behavior, after watching over the whole world for such a long time he could reasonably expect what a human would risk for love. As a calculated program he was not supposed to take so much risk.
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