A Wrinkle in Time is no The Lion, the Witch, and the Wardrobe, but religious language and imagery does keep popping up. Is it coincidence that Charles Wallace asks Calvin to read him the Book of Genesis as a bedtime story, followed by Calvin and Meg taking a walk in the garden, where they both snack on apples? Perhaps...or perhaps these religious allusions are there to create the sense that these characters are about to gain a greater knowledge of good and evil.
Then there's Mrs. Whatsit, Mrs. Who, and Mrs. Which, who were once stars, but also, when Calvin is trying to explain them to the beasts, are best represented as "guardian angels" and "messengers of God" (11.113). The first fighter of darkness that Mrs. Who prompts the kids to name is none other than Jesus, and she quotes from First Corinthians when she's sending Meg off to extract Charles Wallace from the clutches of IT. And when Mrs. Whatsit translates the song of Uriel (which shares its name with an angel), it's a hymn singing the praises of God that quotes from the Book of Isaiah in the Bible (4.94).
Even Mr. Murry gets into the act, after he tessers Meg and Calvin off of Camazotz:
"We were sent here for something. And we know that all things work together for good to them that love God, to them who are the called according to his purpose." (10.68)
So why all the religious-talk? Well, this is, after all, a battle between good and evil, and since its inception Christianity has claimed a large stake in that conflict. The novel makes much of the limitations of one civilization's language: perhaps the characters are just making use of the language they have for talking about good vs. evil. Or perhaps it's the specter of communism again (see the above discussion of Camazotz and IT), since that conflict was often portrayed as Christian democracy vs. godless communism. The novel never makes the role of religion in its world entirely clear, so in the end it's up to the reader to decide how literally to take the text's Biblical allusions.