Suppose it is absolutely true that atheism has a negative impact on your happiness and lifespan. Suppose furthermore that you are the first person in your society of relatively happy theists who happened upon the idea of atheism, and moreover found absolute proof of its correctness, and quietly studied its effects on a small group of people kept isolated from the general population, and you discover that it has negative effects on happiness and lifespan. Suppose that it -does- free people from a considerable amount of time wasted - from your perspective as a newfound atheist - in theistic theater.
Would you spread the idea?
This is, in our theoretical society, the emotional equivalent of a nuclear weapon; the group you tested it on is now comparatively crippled with existentialism and doubt, and many are beginning to doubt that the continued existence of human beings is even a good thing. This is, for all intents and purposes, a basilisk, the mere knowledge of which causes its knower severe harm. Is it, in fact, a good idea to go around talking about this revolutionary new idea, which makes everybody who learns it slightly less happy? Would it be a -better- idea to form a secret society to go around talking to bright people likely to discover it themselves to try to keep this new idea quiet?
(Please don't fight the hypothetical here. I know the evidence isn't nearly so perfect that atheism does in fact cause harm, as all the studies I've personally seen which suggest as much have some methodical flaws. This is merely a question of whether "That which can be destroyed by the truth should be" is, in fact, a useful position to take, in view of ideas which may actually be harmful.)
Would you kill babies if it was intrinsically the right thing to do? If not, under what other circumstances would you not do the right thing to do? If yes, how right would it have to be, for how many babies?
EDIT IN RESPONSE: My intended point had been that sometimes you do have to fight the hypothetical.
You've brought in moral realism, which isnt relevant.
"Would you do X, if it was epistemically rational, but not instrumentally rational"
"Would you do Y if it was instrumentally rational, but not epistemically rational"
If two concepts arent the same under all possible circumstances, they aren't the same concept. Hypotheticals are an appropriate way of determining that.