If it's as early as X2 that Sigma mentions Wily, then that means that possibly before the events of X1 did Sigma 'know' of Wily. 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 don't think Wily is steering away from Zero though. I think it's just a matter of circumstances. I don't think Wily would have thought that Zero would have lost a battle and then have the virus transfer to another robot, but it happened, so he could be working with what he's got.