The Duke study doesn't show believers become more stupid? It shows that very religious and very non-religious people may, generally, have a smaller hippocampus. A smaller hippocampus is associated with hyporeligiosity in some conditions, but away from those it "has been linked to clinical outcomes, such as depression, dementia, and Alzheimer's Disease". The study, as the full length article in Scientific American points out, doesn't show causation. Stress factors related to religion are proposed, to help explain why this also seemed to be something which non-believers have. I found it interesting that people who meditate seem to have a larger hippocampus.
Link to study itself: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017006