I suddenly (and randomly) thought of this today:
In the first Matrix, as Cypher is about to pull the plug on Neo, he tells Trinity that if Neo really is The One, “There would have to be some kind of miracle to stop me! Right?” Of course, a miracle shows up and Tank proceeds to fry the shit out of Cypher.
Previously in the movie, we’re led to believe that The One is some sort of divine intermediary, that he is interwoven with fate itself.
But in The Matrix: Reloaded, that is tossed out of the window. The One is merely a machine-manufactured balance to The Matrix. There is no fate, no overriding divine will. It’s all chance.
Thus, we can conclude that Cypher really could have killed Neo right then and there. While it would have made for a boring series of movies if that happened, it’s still entirely possible as there’s no reason Neo has to be alive. It’s just an interesting turn of events in retrospect- that there was never a big plan to things, and that all the talk of “miracles” and “saviors” is really just a hoax.
But maybe I’m overanalyzing things.