Neo is not a program. If Neo were a program, he wouldn't love, he wouldn't be able to leave the Matrix. If we are assuming MWAM to be true, yes, it is possible, but very unlikely. Why would we see a program talking to the Architect, if the program could just open any ole door, go through, set up a bomb, and then, when the bomb blows up, fly out the windows and tell the humans its all a lie? No, it is very unlikely that we learn so much about Neo, and see his PERSONAL life *cough cough*, if he is not really human. Also, we dont know he is the same in all generations, he could be a totally different person. PLUS, we must assume that all the others were children "we have a rule, we never free a mind once its reached a certain age." Yes, only programs are allowed to RETURN to the Source; this is Neos first time. the "code" Neo carries is the code of the anomaly, that is replaced, so to speak, when Neo died. Also, i believe Neo was able to stop the sentinels beause Zion world is a program, another form of controlling the humans. And, no, Morpheus would NOT be able to go to the Archies room, 1) because he is not the One, which means if he opens the door, BOOM 2)Morpheus is only human, he would instantly be killed if the Source tried to remove the code and instead took out his mind instead.
Regarding the EMP...The ship has to be turned off before the EMP is triggered, otherwise it will fry the circuitry of the ship as well... "Remember in M1, when the squidy shows up, and they turn off the core before charging the EMP?
And im not even going to worry whether the is a difference between human and machine conciousness...