Yes, your ideas certainly make sense BH08685, but I believe that it wouldn't make sense for the machines to use actual 'robots' to be plugged into the Matrix. Using programs (that have no corporeal form) would make much more sense. Why would you use something (or someone), that has all this extra programming to move around actuators and to accept all this input from sensors and such? It'd be very (unnecessarily) bulky. That's why I think he (and perhaps the other ones) are programs, specifically written for inside the Matrix. It also explains why the real Agents have these 'body-takeover'-powers. The Merovingian (and others) certainly don't have these things ;)
But you do certainly raise the interesting point: Where would Smith have gone (before he went 'nuts'

) if Zion was destroyed? Perhaps he would see suicide as salvation? (I don't believe so.)