They were not removing them. They were cleaning them and closing them off. They cannot be removed. In the first Matrix, after Neo wakes up on the Neb after surgery, there is a scene of him pulling an IV out of a wrist plug. Also note that Morpheus and Trinity ALSO have their plugs throughout.
-- They clearly set the stage for Revolutions by opening up discussions of the balance of POWER and relationships between man and machines.
Not just that, but also the interdependance between man and machines. Also the fact that this is irrelavent in the grand scheme. That the only thing that really matters is who is in control of who. Of course, it also touches on the ethic inherent in use of power as well as the fact that all appearances of control are illusions.
Question: where are the kids in Zion?
Watch the "pilgrim" scenes closer when they get to Zion. Lots of children.
Pull back a step from that, and you'll see that the relationship between man and machine is caught in an endless loop - a system anomally.