Hawthorne makes clear in this passage that it is religious intolerance that drives Endicott and the other Puritans in destroying Merrymount. The particularly cruel and unsavory quality of Endicott's narrow-minded views is expressed in his willingness to shoot the poor bear.
"It must be for the Great and General Court to determine, whether stripes and long imprisonment, and other grievous penalty, may atone for his [the Merrymount minister's] transgressions. Let him look to himself! For such as violate our civil order, it may be permitted us to show mercy. But wo to the wretch that troubleth our religion!"
"And this dancing bear," resumed the officer. "Must he share the stripes of his fellows?"
"Shoot him through the head!" said the energetic Puritan. "I suspect witchcraft in the beast."