Actually, I should be more clear. Let T = theism, H = theism makes people happier, L = lots of people are theists. Then H&L are evidence for T iff the quotient P(H&L|T)/P(H&L|~T) > 1. We can rewrite this quotient as P(L|H&T)/P(L|H&~T) * P(H|T)/P(~H|T). Then the thread-starter's argument at best shows that T is irrelevant to L once we know H, hence P(L|H&T)/P(L|H&~T) = 1. So in this best-case scenario, the quotient becomes P(H|T)/P(H|~T). If theists can show this is greater than 1, then H&L still ends up as evidence for theism. So that's what you really have to be asking.
Religion apparently makes people happier. Is that evidence for the truth of religion, or against it?
(Of course, it matters which religion we're talking about, but let's just stick with theism generally.)
My initial inclination was to interpret this as evidence against theism, in the sense that it weakens the evidence for theism. Here's why:
We could also put this in mathematical terms, where F represents an increase in the prior probability of our encountering the evidence. Since that prior is a denominator in Bayes' equation, a bigger one means a smaller posterior probability--in other words, weaker evidence.
OK, so that was my first thought.
But then I had second thoughts: Perhaps the evidence points the other way? If we reframe the finding as "Atheism causes unhappiness," or posit that contrarians (such as atheists) are dispositionally unhappy, does that change the sign of the evidence?
Obviously, I am confused. What's going on here?