My interpretation of that scene has always been the opposite.
The one is supposed to:
The function of the One is now to return to the source, allowing a temporary dissemination of the code you carry, reinserting the prime program. After which you will be required to select from the matrix 23 individuals, 16 female, 7 male, to rebuild Zion
Bold mine. The one, as explained by the Architect, has always had a strong connection to humanity by design, however Neo's case is different:
Your five predecessors were by design based on a similar predication, a contingent affirmation that was meant to create a profound attachment to the rest of your species, facilitating the function of the one. While the others experienced this in a very general way, your experience is far more specific. Vis-a-vis, love.
This, is a problem. The previous incarnations of the one followed the logic of the architect, the only way out for the survival of the species was to follow suite. That would mean the destruction of Zion but the survival of everyone connected to the Matrix.
However, for Neo, his specific love for Trinity is an issue as she will be one of the casualties if Neo goes back to the source. The architect is trying to get rid of that variable in the equation, if she's alrady death, then there's nothing for Neo to go back to or prevent him from completing his mission. He goes extra lenght to assure Neo that she's going to die no matter what he does, therefore eliminating the hope and the love and, in his view, leaving only one option remaining... to go back to the source and restart the cycle.
The Architect - Which brings us at last to the moment of truth, wherein the fundamental flaw is ultimately expressed, and the anomaly revealed as both beginning, and end. There are two doors. The door to your right leads to the source, and the salvation of Zion. The door to the left leads back to the matrix, to her, and to the end of your species. As you adequately put, the problem is choice. But we already know what you're going to do, don't we? Already I can see the chain reaction, the chemical precursors that signal the onset of emotion, designed specifically to overwhelm logic, and reason. An emotion that is already blinding you from the simple, and obvious truth: she is going to die, and there is nothing that you can do to stop it.
The architect sees the issue and tries (unsuccesfully) to convince Neo. In the end Neo's love for Trinity ends up being an unforseen event by the architect. This will lead (at least on my read of the movies) to the new "plan" forged by the Oracle with the approval of the architect and the machines.
