The old Necron codex did say that "most" of the Necrontyr were taken in by the Deceiver, not all. It is conceivable that a small group escaped, settled an out-of-the-way desert planet (thereby escaping the notice of their undead brethren), eschewed technology and what they called themselves for the same reason, and kept the vast majority of the population ignorant and isolated in order to keep off the radar, so to speak. A small group of elites would keep apart from the general population and preserve what they could of science and technology, just in case the right moment came.
When the Imperium showed up, the elite group (Ethereals) saw that by virtue of another race besides Old Ones and Necrons even existing that meant that both the former were either dead or no longer powerful in any meaningful sense. Their sudden appearance to the now Hunter-gatherer Necrontyr (or "Tau") and the subsequent massive upsurge in technological innovation strongly point to this conclusion. The fact that an obviously Necron artifact like the Dawnblade was able to be wielded without killing its user, but still corrupted his mind, lends credence to the idea that the Tau are the descendents of the only survivors of the robotic transformation of the Necrontyr.
The emphasis by the same Ethereals on "the greater good" would come from the desire not to repeat the same ambition-driven drive to dominance and physical immortality that compelled their ancestors to make a deal with the Devil (literally). It represents a turning away from the dark side of their natures in service to a noble (enough) cause. That was the cause for overwhelming concern when Shadowsun showed up to the Ethereal council carrying a Necron weapon and boasting about his personal genius and ruthless tactics, which got him exiled immediately.
Also, as an aside, the word "Tau" itself could have been taken from the "T" in the last part of "Necrontyr", ("Tau" is the Greek word for the letter "T"). Obviously the Necron part would be odious to those who saw what happened to their people at the hands of the Deciever, but some identity with the original people would be desired, so the distinguishing "T", or "Tau" was kept.