Zero doesn't need X's circuitry designs to adapt to a new code of morality and ethics, robots like Ballade and King previously set the standard for that kind of growth, and without X's extreme form of worrying which good Zero doesn't seem to match with regardless. The ability for Wily to design a smart robot that learns and adapts beyond its origins is already in place.
But supposing Wily is (somehow) copying Light's latest brain designs thinking that they will give some fast-processing edge despite that Light's purpose in the worrying design is to allow the robot be intelligent and sensitive enough to avoid the kind of unethical activities that Wily routinely assigns to his robots, then Wily has some serious adapting to do to suit his purposes. If the worrying is the work of a single chip vs the entire brain, better to just chuck that out and create his own evil version of that chip in its stead. If this is a more general and integrated programming algorithm, then with cutting pasting and splicing evil code which eventually becomes known as the virus is the method of choice. In either regard Zero's eventual heroism is not by default, but by some manner of error or miscalculation. The good side is not meant to be operating without or above the evil side, for the evil as the "true" form is desired above all, and Zero operating without this in firm place is to Wily essentially broken and malfunctioning.
How it came to be malfunctioning is the semantic scene-stealer. If Wily's evil code was never properly a match to cancel out the more noble effects of the circuitry, if that "W" in the X4 flashback scene was the rejection of the darkness or an error of ethical conflict arising, then it was perhaps inevitably Wily's failure inherent in design. Never properly managing to counteract that which he himself had dangerously set into his creation, Wily played with fire and got burned, with none to blame but himself.
Yet contrary to that lies the effects of the virus whose influence can be seen on the vast numbers reploids who are known explicitly to be inheriting some of X's circuit designs and even simpler mechaniloids who are not. One would ask why it works so well on so many but not on the one it was designed to be integrated with in the first place. But in fact, for a while at least, it does seem to work. Zero's evil persona is working fine, at least up until the "W" lights up. In X2 Serges can make it work again for a time, and X5 as well. It would seem then that the concept he utilized is sound in theory, if not yet perfected. The extremes to which must be gone to achieve it grow seemingly greater, the element in Zero which refuses the process perhaps grows stronger.
It is also possible that the "W" was related to some other ill-timed anomaly. Perhaps a triggered memory of Wily from during construction not unlike X's flashback in Day of Sigma, but meant to gain Zero's attention and push him onto destiny's path. Or Wily himself brought back to life by the virus from data within Zero's head, or attempting to communicate with Zero directly into his mind. If something of this nature, Wily's evil programming was still a success, maybe more than Wily himself had dreamed. Only the timing of the situation is amiss.
When applying Inafune's statement, the first hypothesis includes only the circumstance of Wily's design failure at an unfortunate moment, denying Sigma or Cain's presence being necessary or even an influence in the change within him. The latter more heavily relies on the combination of Sigma's involvement in the scenario, damaging Zero's brain and inadvertently siphoning the virus programming into himself, possibly ejecting the spirit form of Wily as well. Without memories and bloodlust Zero can adapt himself anew to the world, but without Sigma being there to take advantage of Zero's momentary weakness there well could have been no such change for the long haired god of destruction.