Hmmm. I don't think he 'revived' him any literal sense - maybe it's something like Light's hologram, an semi-AI of him merged into the virus itself (I mean, think about it, they say all geniuses put a piece of themselves into their masterpieces ...) That way, Wily can keep an eye on Zero and basically have a front row seat for his 'revenge'.
As well all know, I like the idea of Zero rebelling and forcing out the virus on his own. Because Zero's essentially a child with an extremely under-developed mind; of course something like the virus would just make him go utterly ape-shit, his brain isn't advanced enough to do anything else! So naturally, when Zero forces him out the virus/Wily takes his chances and leaps into Sigma.
And following from that train of logic, that means that Sigma is just a means to an end; Wily wants Zero back. But because of Zero being taken out and reprogrammed, it's going to be tricky to get him back. But think about it. Sigma starts huge wars and such, and who exactly comes running straight to him? Right, Zero. I figure the reason Wily helps out Sigma during the wars is so he can create basically a giant trap for Zero to fall into (and he eventually does, in X5).
But I don't want to say that Sigma's just a poor helpless puppet. I hate it when major villains are just victims. I figure that Sigma is fully in control, making fully educated choices about destroying humanity. Wily has just got his own secret agenda. Sigma keeps asking Zero to 'join us' and such, so he knows about Wily's plan - just not the part that Wily is willing to sell him out to do so (or he does know, and has his own plan).
So yeah, that's my take on the whole idea. Personally, this new twist just gives me a headache.