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There's also a strong possibility that the section was cut as part of a massive series of edits L'Engle went through in trying to get her manuscript published. A Wrinkle In Time was rejected by several publishers, many of whom thought the book was too complex for kids. Even when John Farrar of Farrar, Straus and Co. decided to move forward with the book, he warned L'Engle not to be disappointed by what he thought would likely be slow sales.
The easy answer is that the pages were cut because they outline too clearly some political beliefs within the story. L'Engle name drops not only Hitler, but Khruschev, Mussolini, Mao, and Castro. And while calling out some historical monsters isn't such a bad thing to do, it's a lot more politically-charged than a lot of L'Engle's work.
This sick longing for security is a dangerous thing, Meg, as insidious as the strontium 90 from our nuclear explosions that worried you so...