It could work like that (though there were no conversion here). This kind of mob mentality can and do manifest itself over other channels than religion of course, but I think atheism is a less likely channel than religion itself.
Religion generally comes with a moral system, backed up by a set of beliefs. Among them, the belief that it is proper and good to believe (and, well, you know). It also comes with community by default, which can have a strong effect (compare r/atheism and r/religion: the more united tribe (atheists) sound much less tolerant overall).
The reason why someone turned to atheism may also influence his likelihood of persecuting believers. A Lukeprog scenario isn't likely to result in intolerance, for instance. Raw rebellion, followed by a "this is all bullshit anyway" rationalization may. I'd put being raised by atheists parents between the two, though it depends on the parents.
Anyway, I think the strongest factor is mob mentality. A group of anything that doesn't identify itself as such isn't very likely to make others miserable because of that "anything". And more often than not, atheists form such a group.
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?