Zordon, despite being very, very good, might not have an infinite amount of "good energy" to throw around. The villains might have had so much "bad energy" that the "good energy" got tapped out before frying them completely.
Think of it as shielding against an atomic blast; evil villains with a paper-thin amount get a complete, "turn-to-ash" level of "good energy", but having a foot-thick lead-lined amount means you get your bad energy burned out/off of you, turning you human since you no longer have any "bad energy" making you an evil villain.
This way of thinking also accounts for any other "high-level" villains you think should have survived; Zordon's "good energy" was expended turning them to ash, meaning less energy to try and burn out Rita, Zedd, Divatox, and Astronema.
EDIT:
To show some research, and to highlight that Zordon might not have infinite energy, The wikipedia article states that
Zordon is captured by Dark Specter, who slowly drains him of his powers.
it also mentions that
Zordon's death creates an energy wave which travels throughout the universe
This could mean that the energy emanates out in a similar fashion to a nuclear explosion, which would support the above analogy.
the Lord Zedd wikipedia entry also details that
[Zedd's] son, Thrax, had been sealed in a space dumpster by the Sentinel Knight.
Thrax had been presumably shielded from the "good energy" by said space dumpster, again in an analogue to nuclear radiation shielding.
Hope that satisfies somewhat.