"Extinguish" also means "put an end to; kill"--although the example sentence is using the word to describe the darkness that might have come from the extinguishing of the moon, this other definition could fit how Meg thinks about what is happening to her, as she loses her grips on light, sound, and feeling.
Did a shadow fall across the moon or did the moon simply go out, extinguished as abruptly and completely as a candle?
And this feeling of moving with the earth was somewhat like the feeling of being in the ocean, out in the ocean beyond this rising and falling of the breakers, lying on the moving water, pulsing gently with the swells, and feeling the gentle, inexorable tug of the moon.
"Apprehension" also means "the cognitive condition of someone who understands"--this would not fit Meg's feelings in the example sentence, but it describes the state that Meg will be in after Mrs Whatsit transforms into a beautiful creature that takes them on a journey through the air.
“Sshoww themm,” she said to Mrs Whatsit, and at something in her voice Meg felt prickles of apprehension.
a state of being carried away by overwhelming emotion
"Exaltation" also means "the elevation of a person, as to the status of a god"--Calvin would agree with this definition because, while Meg is overwhelmed by the joy she sees, he falls to his knees in front of the transformed Mrs Whatsit. But Mrs Whatsit would disagree because she recognizes the existence of God, so she tells Calvin to stand up.
She was a marble white body with powerful flanks, something like a horse but at the same time completely unlike a horse, for from the magnificently modeled back sprang a nobly formed torso, arms, and a head resembling a man’s, but a man with a perfection of dignity and virtue, an exaltation of joy such as Meg had never before seen.
having the character of a loud deep sound; the quality of being resonant
The resonant voice rose and the words seemed to be all around them so that Meg felt that she could almost reach out and touch them: “Sing unto the Lord a new song, and his praise from the end of the earth, ye that go down to the sea, and all that is therein; the isles, and the inhabitants thereof.
thrown into a state of agitated confusion; (`rattled' is an informal term)
"Perturbed" is an antonym of "serene" ("not agitated; without losing self-possession")--but in these two sentences, the unperturbed Calvin is ranked as slightly less self-possessed as the serene Charles Wallace, and they both stand in contrast to Meg, who sighs sadly at her inability to understand how people can save time by traveling across wrinkles in time.
Charles Wallace accepted the explanation serenely. Even Calvin did not seem perturbed.
tending to increase knowledge or dissipate ignorance
"Illuminate" means "make lighter or brighter"--similar to the next example sentence, where comprehension is connected to light rather than darkness, here Meg's understanding is connected to a brightness in her face and an excited happiness in her actions.
For a brief, illuminating second Meg’s face had the listening, probing expression that was so often seen on Charles’s.
dangerous to health; characterized by progressive and uncontrolled growth (especially of a tumor)
The coldness deepened and swirled all about her and through her, and was filled with a new and strange kind of darkness that was a completely tangible thing, a thing that wanted to eat and digest her like some enormous malignant beast of prey.