Well, 268 subjects isn't a lot of people to study for much of anything. Also, they hypothesize that the "stress" of being "outside the mainstream" as far as religious beliefs causes the shrinkage. I didn't see any mention in the article where they looked at other sources of stress in the subjects' lives. As someone else mentioned, financial status or problems could be a source of stress, but so could a lot of things (such as being a caregiver for an ill family member, having losses in one's life, and so on and so forth).
There are an awful lot of variables to control for to make this sort of study meaningful and I'm not reading where they did that.
"Psychosocial and demographic covariates were included in these analyses, as well as baseline total cerebral volumes as a proxy for head size. Psychosocial factors assessed included stress (global self-reported stress experienced over the past 6 months), social support (a composite variable, primarily level of satisfaction with personal relationships [55], [56]), and depression status (membership in depressed or non-depressed group). Demographic factors assessed included age, sex, self-reported race (dichotomized as white and non-white), years of education, and duration in the study." -
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0017006