"Believe me, it gives us no pleasure to destroy men's faiths, but all the world's religions cannot be right, and they know it. Sooner or later man has to learn the truth: but that time is not yet." (2.82)
Religion as a source of truth and morality becomes obsolete when the Overlords arrive. As the quote says, they couldn't all be correct, and given the existence of the extraterrestrials, you'd think a prophet or two might have mentioned them.
Their interminable poker games were punctuated with violent political arguments, and it soon became obvious to Stormgren that the big Pole had never thought seriously about the causes for which he was fighting. Emotion and extreme conservatism clouded all his judgments. (3.79)
In Childhood's End, the source for morality is not centered on feelings or emotions, but on reason and thinking. This isn't to say that emotions don't have a purpose—there are still diehard sports fans in the future—it's just that ethics are not based upon them.
There were some things that only time could cure. Evil men could be destroyed, but nothing could be done with good men who were deluded. (4.96)
An interesting aspect of Childhood's End is that there really aren't any "bad guys" in the story. Instead, a couple of good men feel that other men are deluded, and vice versa. Which leads us to the Buffalo Springfield quandary: Is nobody right if everybody's wrong?
Of the faiths that had existed before the coming of the Overlords, only a form of purified Buddhism—perhaps the most austere of all religions—still survived. The creeds that had been based upon miracles and revelations had collapsed utterly. (6.28)
Going back to the first quote for this theme: Miracles and revelations succumb to the idea that reason is the true source for morality in this novel. Calling Buddhism the most austere of all religions is a judgment call on the part of the narrator, but hey, it's his story.
It was strange, Karellen thought, that so many human beings still seized every opportunity for primitive behavior. They could reach the bottom of the canyon in a fraction of the time, and in far greater comfort, if they chose. Yet they preferred to be jolted along tracks which were probably as unsafe as they looked. (9.3)
Primitive behavior is a source for many of the aspects of humanity that puzzle the advanced and sophisticated Overlord. One could argue that ethics and morality are also primitive behaviors that Karellen cannot understand. After all, do we ever see Karellen do anything we could truly consider moral in the story?
The existence of so much leisure would have created tremendous problems a century before. Education had overcome most of these, for a well-stocked mind is safe from boredom. (10.5)
If reason and thinking are the sources of true morality in the novel, then how would someone foster a sense and understanding for that morality? Education, naturally.
"Good: I'm glad to see that you've been into the problem thoroughly, and aren't treating it like some stunt you can back out of if you don't like the way it's going. It's your life you're playing with, but I'd hate to feel I was helping you to commit suicide." (12.27)
Sullivan is a scientist, but he's no Frankenstein, throwing morality to the wind to delve deeper into the mysteries of life and the universe. Instead, he's interested in furthering science but not at the expense of his moral core. Sending Jan to his death would be totally against said moral core.
"Everybody on this island has one ambition, which may be summed up very simply. It is to do something, however small it may be, better than anyone else. Of course, it's an ideal we don't all achieve. But in this modern world the great thing is to have an ideal. Achieving it is considerably less important." (17.29)
The morality of Athens is to further a discipline—theater, painting, literature, and so on—by having an ideal. You've got to give them credit: That's a pretty unique way to answer the ethics question.
"I must take [the children] away and isolate them, for their protection, and for yours. Tomorrow my ships will begin the evacuation. I shall not blame you if you try to interfere, but it will be useless." (20.25)
Karellen's morality, like Karellen himself, is pretty foreign to what we consider morality. Taking children away from their parents is pretty hardcore and unmoral for people, but Karellen sees it as the only possible action. Again we wonder whether morality even applies to aliens.