He will not destroy them. He can't.......The Matrix must survive for the 6 Billion people connected to it to survive.
The machines never wanted a war. They wanted to live together in peace as equals.......the humans are the ones who wanted war. I have a feeling he will somehow convince the machines that the systems of control they currently use are no longer needed as machines and man can finally live together in harmony. This ofcourse will spare the lives of all those connected to the Matrix........and will save Zion as the only reason the machines destroy it is as a measure of control for "the one".
Also.....movie is 1hr 28 min. long........not 2.5 hours.