There are two doors. The door to your right leads to the source and the salvation of Zion. The door to your 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 are going to do, don't we? Already I can see the chain reaction, the chemical precursors that signal the onset of an 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 you can do to stop it.

The Architect offers Neo the choice to save Trinity and kill everyone including the machines or return to the source and in so doing ultimately service the machines.