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Some questions to ask:
(I've recently joked that SIAI should change its motto from "Don't be jerks" to "Be less evil than Google".)
"Am I making people stronger, or weaker?" That's a very important question, and sometimes hard to get right.
Consider a theist for whom the belief in god is a fundamental aspect of his life, whose faith makes him strong because it gives him something to protect. Breaking (or weakening) his belief in god before he built himself a line of retreat can do much more harm than good.
What should be done is first building the line of retreat, showing him that even without a god, his life does not become pointless, his ethics won't crumble to dust, and the...