It's just as well this passage was cut. Can you imagine this book having had any kind of readership in America had she dared be critical of the U.S. in her writing at the height of the Cold War?!
The book would have been burned in McCarthyist witch-hunts, she would have been arrested as a communist sympathiser.
She only had to substantially obfuscate the message of her book to manage to get it published in a backwards, repressive regime which fancies itself as a bastion of freedom.
Your speculations about what "would have been" – book burnings! imprisonment! – are ahistoric to the point of paranoid nuttyness.
The specific passages left out were a few slight intensifications of one theme. Leaving them out didn't 'obfuscate' anything. As the literary critics consulted by the WSJ suggest, the cuts arguably improved the book's narrative flow and timelessness.
Also note that by 1962, when Wrinkle in Time was published, the country was already 8 years past the peak of McCarthyism, with McCarthy discredited and dead. Even at the height of McCarthy's investigations, in the early 50s, the only metaphorical "book burning" that happened was the State Department pulling some books from its overseas outreach libraries.
That's an embarrassment, of course, but not the kind of persecution you're implying that L'Engle would've faced.
For cultural context, The Twilight Zone's original TV run was 1959-1964. It often featured the exact same kind of allegorical criticism of conformity and paranoia. A few extra words in Wrinkle in Time – about how even in democracies, "the sick longing for security is a dangerous thing" – would've been zero risk to the book's popularity or author.
There have been a lot of "book burnings" since 1960. The subject du jour to ban shifts slightly over the years, from racial issues to gender equality to same-sex marriage, but parents often end up in a frenzy over one thing or another.
Nothing about these elided Wrinkle in Time passages were especially controversial, then or now.
Other parts of Wrinkle in Time, in particular mentions of Jesus as sort-of coequal with other artists and scientists or Buddha, or its not-quite-Christian mysticism, have sometimes run afoul of some religious parents' groups.
But a few generic warnings to the effect that "craving total safety can be dangerous"? That's pretty much common wisdom, in any American era, and doesn't trigger claims of insult or depravity.
Others have already done some explaining, but I'd like to point out that the 1950s conformism thing has kernels of truth, even large kernels of truth, but you also have to account for the fact that the rebellion of the 1960s itself had to write a mythos of excessive conformity to justify itself. As is often the case, it overstated its case, because in the aggregate, social movements are really bad at restraint or subtlety. You must remember that the 1950s are still the era that gave birth to the 1960s et al, and it's a great deal more complicated than "the kids just rebelled for the first time in the entire history of man for no apparent reason".
Ironically, it is now this very 1960s rebellion that we still live today that is now entering an accelerated and probably inevitable disintegration of its own as it itself becomes an ideology of stultifying conformity. History is not without its ironies.
I'm trying to determine what would have been construed as being critical to the U.S. in that passage.
National Socialism had been voted into power in Germany through legitimate means just a couple of decades prior to the book being released. I doubt it'd be taken as an implicit critique in pointing out that even democracies can be abused. After all, it was this realization during the formative years of the U.S. that lead to measures such as the Bill of Rights.
"Stranger in a Strange Land" was published in 1961, blasting established religion and conventional sexual morality. It wasn't a YA book but it certainly refutes the idea of the cultural censorship you assert.
It did start out as a YA book. Only, halfway through, RAH realized that he wanted to publish to a more mature audience. The first third of SiaSL hearkens back to his YA beginnings; the rest of it appeals to the rebellious. That book cemented my enjoyment of the rest of his writings because I bridged from child to adolescent at the time of reading.
'53. It got a very short initial run resultantly, and there was a lot of talk in the papers about the "controversy" of witchcraft, in order to shift the debate away from the contemporary context.
Sure, it may not have resulted in book-burning (do allow me some hyperbole!), but I stand by my point that had that passage remained, this would not be a staple of American youth reading today, and the book would have ended up either obscure or "controversial".
The book would have been burned in McCarthyist witch-hunts, she would have been arrested as a communist sympathiser.
She only had to substantially obfuscate the message of her book to manage to get it published in a backwards, repressive regime which fancies itself as a bastion of freedom.