It's not so much that the author/maintainer has done something wrong here, as that, if it's being treated as the author's personal religious space rather than an open and nondiscriminatory work environment, other projects/orgs should not be depending on it.
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If you're working for an org that produces software built on sqlite and need to submit bug reports or patches as part of your job, your employer should not be requiring you to do that with an upstream that wants you to follow a religiously-based CoC.
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Maybe I'm missing something but I think there's still a need for interaction within the scope of a CoC when you use the library in a major piece of software.
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I wouldn't feel welcome in a project with that Code of Conduct due to being an atheist. I expect many devout Christians, Muslims, etc. feel the same way about a Code of Conduct that I'd support though.
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People are pushing a Code of Conduct treating religion as a protected class (for better or worse) and asking to respect other viewpoints, but they're not. I'm finding it a bit ridiculous to call out SQLite and direct harassment towards them while claiming to believe in that.