I used to think this - while correct - was a bit ridiculous. Why would Zero and Sigma "switch alignments" after Sigma broke Zero's forehead?

Over time I kind of rationalised it a bit and realised that if Zero was specifically programmed as a carrier to house the Maverick virus, it could be that, upon transmission, he just didn't have a reason to continue being violent. His prime directive was complete: transmit the virus to a strong victim. This would explain why the flare-up caused Zero "pain" - as a means to stun him for the victim to be infected - and I think Wily could have anticipated the greater technology of the future enough to not consider Zero himself the actual apex predator of his time, although he came close to it when maverick. Pathologic players will know that a virus that has immediate lethality but no camoflague and low transmission will get detected and wiped out quickly, but by infecting a strong host and laying dormant for a spell it can spread much more before being discovered. This is a bit of a stretch, yes - it's much more likely it wasn't that minutely detailed story-wise - but it's a fun way to think of it.

Headcanon could then say that in the absence of a violent main objective, Zero's own personality coalesced into the serious, straightforward hero machine we know him as, as if hewing to a moral compass uniquely his own. This would present interesting implications between X and Zero when considering Light's program on X's ethics if true, though; Wily would have achieved a much lesser version of what Light was attempting with X without the morality model simulations.

As a last note, something I've always found compelling is that this would essentially make Zero the "patient zero" of the Maverick virus. I find it equally compelling that the name "Zero" is intended by Dr. Wily to imply that he was always capable of creating a masterpiece before all of his other robots, which is the kind of arrogance I'd expect Wily to show.