I would like to say that maybe it was Wily (voice, personality, etc.) in the form of the virus that was making Zero Maverick and once that was transferred to Sigma, he could have put up a fight, but then he would have eventually started 'talking back,' listening to Wily and becoming more and more Wily's slave.
I think you're on to something. I'm liking this idea. Though I also agree with BB that it makes things way too simple if Sigma is just a helpless patsy of the Virus. They're clearly -collaborating-, so even if the virus accelerated something already at work inside Sigma, it's still something he's doing of his own accord. (Although it'd sure be hilarious if the forerunner of the Reploid independence movement is just a wicked human's patsy to destroy other humans in the end after all...)
It occurs to me that if something was wrong with Zero at the start, Wily (being true to his name) as a Avatar Of Evil (tm) might have jumped into Sigma just to get Sigma to rebuild/repair Zero...?
I don't know. It's sort of far-fetched, that idea and I'm not explaining it well because I'm in a hurry. Maybe more on this later...