The closest I have found to this is indeed in Cryptonomicon. I don't have a page number because this is a Kindle book, but it is towards the end of the chapter titled Home, a little over halfway through the book. The passage is:
The friendliest and most sincere welcome he’d gotten was from Scott, a chemistry professor, and Laura, a pediatrician, who, after knowing Randy and Charlene for many years, had one day divulged to Randy, in strict confidence, that, unbeknownst to the academic community at large, they had been spiriting their three children off to church every Sunday morning, and even had them all baptized.
Randy had gone into their house once to help Scott wrestle a freshly reconditioned clawfoot bathtub up the stairs, and had actually seen the word GOD written on actual pieces of paper stuck to the walls of their house—like on the refrigerator door, and the walls of the children’s bedrooms, where juvenile art tends to be reposited. Little time-wasting projects they had done during Sunday school—pages torn from coloring books, showing a somewhat more multicultural Jesus than the one Randy had grown up with (curly hair, e.g.), talking to little biblical kids or assisting disoriented Holy Land livestock. The sight of this stuff around the house, commingled with normal (i.e., secular) kid-art-junk from elementary school, Batman posters, etc. made Randy feel grossly embarrassed. It was like going to the house of some supposedly sophisticated people and finding a neon-on-black-velvet Elvis painting hanging above their state-of-the-art Italian designer furniture. Definitely a social-class thing. And it wasn’t like Scott and Laura were deadly earnest types, and neither were they glassy-eyed and foaming at the mouth. They had after all managed to pass themselves off as members in good standing of decent academic society for a number of years. They were a bit quieter than many others, they took up less space in the room, but then that was normal for people trying to raise three kids, and so they passed.
Randy and Amy had spent a full hour talking to Scott and Laura last night; they were the only people who made any effort to make Amy feel welcome. Randy hadn’t the faintest idea what these people thought of him and what he had done, but he could sense right away that, essentially that was not the issue because even if they thought he had done something evil, they at least had a framework, a sort of procedure manual, for dealing with transgressions. To translate it into UNIX system administration terms (Randy’s fundamental metaphor for just about everything), the post-modern, politically correct atheists were like people who had suddenly found themselves in charge of a big and unfathomably complex computer system (viz. society) with no documentation or instructions of any kind, and so whose only way to keep the thing running was to invent and enforce certain rules with a kind of neo-Puritanical rigor, because they were at a loss to deal with any deviations from what they saw as the norm. Whereas people who were wired into a church were like UNIX system administrators who, while they might not understand everything, at least had some documentation, some FAQs and How-tos and README files, providing some guidance on what to do when things got out of whack. They were, in other words, capable of displaying adaptability.
However this is taken no further. There is no mention of going to church acting as a protection against cults.