The amygdala is invovled when guilt occurs because it is scary and emotionally unpleasant to think you have grounds to hate yourself or be socially considered bad. But the amygdala is not the source. You have to have a strong social cogntive aspect to guilt, and that is what the amygdala is reacting to.
Guilt is not like rage or fear. It is a complicated phenomenon where parts of the brain are triggering other parts. As if parts of you brain have taken over the voices of the church or parents or peer groups.
Guilt intensity was associated with activation of the dorsomedial PFC, superior frontal gyrus, supramarginal gyrus, and anterior inferior frontal gyrus. Guilt accompanied by social consequences was associated with greater activation than without social consequences in the ventromedial and dorsomedial PFC, precuneus, posterior cingulate, and posterior superior temporal sulcus. Finally, the interaction analysis highlighted select regions that were more strongly correlated with guilt intensity as a function of social consequence, including the left anterior inferior frontal gyrus, left ventromedial PFC, and left anterior inferior parietal cortex.
from…
ncbi.nlm.nih.gov/pmc/articles/PMC3288150/
Where there is guilt, you once had social threat, which became internalized. People are so fucking scared, and tend not to look at that, because if they knew what guilt was, they might slowly drop it over time. And even considering that is scary. Religions knew how to push buttons with visions of eternal damnation, though there are secular ways of getting the more lobal and advanced parts of your own brain to torture you and your amygdala.