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I fail to see why the whole Matrix is complicated at all.
Follow me here and I will explain.
The machines main source of power is the Matrix (the people connected to it)
Morpheus has stated that if you are not one of us you are one of them and most of the people in the Matrix could not be freed anyway and if you die in the Matrix you die in real life.
As the Resistance can take in any weapons they choose through the Loading program, why not just take in a load of high yield nuclear weapons and kill everyone on the Matrix Earth, its not like the machines could stop them as Neo could just stop them.
There we are I have just saved humanity.
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