The religious tend to take a dualist approach to these kinds of results, arguing that these changes in brain activity are somehow just a signal, or only part of the story. The actual spiritual experience is generated somewhere else, and the brain activity is just the physical manifestation.
But this argument crumbles if spiritual experiences can be generated by actively changing brain activity. There is some evidence already that this is so. Most famously, Michael Persinger at Laurentian University has found that using electromagnets to stimulate the temporal lobe can generate spiritual feelings (although recently Swedish researchers were not able to duplicate his results).
So what's the connection to brain damage? Well, a new study by Brick Johnstone and Bret Glass at the University of Missouri-Columbia has found that people with evidence of brain damage to their right parietal lobes score higher on a standard measure of spirituality.
What they did was to assess 26 adults with modest traumatic brain injury (they were all walking wounded, able to function in the outside world) to a battery of tests of brain function. What they were expecting to see was that brain damage in the right parietal lobe would increase spirituality, but that damage to the frontal lobe or left temporal lobe would decrease spirituality.
In fact, damage to the frontal lobe did not seem to have any effect, and although there was a slight signal with damage to the left temporal lobe, it wasn't statistically significant.
Interestingly, the effects of damage to the right parietal lobe match with previous studies looking at brain activity in meditating Buddhist monks. When they achieved a transcendental state, activity in their parietal lobes was also quelled.
So it seems that shutting down this part of the brain seems essential for at least some aspects of religious experiences. Why this particular bit of the brain? Well, it's all to do with how we figure out where we are, and how we relate to the world around us. As Johnstone & Glass explain:
From a neuropsychological perspective, the right hemisphere allows for individuals to define themselves in relation to the immediate environment, the here-and-now. The right parietal lobe is generally associated with awareness of the self relative to other objects in space, awareness of the self as perceived by others in social situations, and the ability to critically evaluate one’s own strengths and weaknesses (such as insight). Disorders of the right hemisphere involve a diminished capacity in the ability of the self to function in the immediate environment, including difficulties localizing the body in space...In other words, it's this bit of the brain that figures out where you are in time and space. If it breaks down, you'll experience some pretty freaky sensations - which, if you are so inclined, the rest of your brain will interpret as a religious experience.
Brick Johnstone, Bret A Glass (2008). Support for a neuropsychological model of spirituality in persons with traumatic brain injury Zygon, 43 (4), 861-874