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West Coast...that's what set off red flags for me, too. The absolute best advice so far has been given by the commenter who wondered if this student is a plant trying to ferret out godless academics to give right-wing "academic Gestapo" groups ammunition. In this climate, that is not a paranoid reaction.
Send this student to whatever version of the United Ministries (main line Protestant, usually a mixture of Methodist, UCC, Presbyterian, Episcopal, and Lutheran) you have on campus. They have a very ecumentical approach to faith. In my student days (late 80s), before I lost my faith altogether, I found our campus's organization to be thoughtful, open-minded, respectful of students' beliefs, deeply understanding of the "dark night of the soul," and above all, kind.
And, speaking as a former academic myself, I also have to warn you against becoming too closely enmeshed in student problems. It's good to know that students feel they can come to you for advice, but it's better to know where to send them for help. Don't tell students what you think. If there's no reason for this reason to have been public before, they have no business knowing your private beliefs. Please watch your professional boundaries; it will help you avoid some sticky situations.