but since both of them lost, the matrix is balanced again, and the machines don't have to worry about it becoming off-balance again. your thought is that the equation is always supposed to be unbalanced, but if an equation is unbalanced, then the equation must be balanced for it to work. the equation must be balanced at all times; this is the point of the Architect. Once Neo was removed by Smith, the equation became unbalanced, so Smith had to be taken out of the Matrix.