Interesting.
Yes Cypher did ask to be reinserted. The question is, how? When he spoke to the agents it was while he was linked into the Matrix through the cranial plug. Why would the Matrix allow itself to be hacked into from the outside world. That would mean that the computer system the "free" humans use would also be part of the A.I. itself.
The End??? I believe the end will be that no one was ever free to begin with. That ALL the humans are still jacked into Matrix and this is the life-reality that the A.I. have given them to give their unconscious mind purpose in order to keep their bodies functioning to create the needed "life-engery" the big machine needs to function.