not a teacher
Conventional wisdom has it that the loss of faith is followed by a plunge into an abyss of despair, after which the new atheist climbs out of the abyss and starts hurting puppies."
The writer is saying that some people believe that a person who becomes an athiest might lose their sense of morality and common decency and start doing nasty things. He uses "hurting puppies" to represent acts of violence against things that are cute and defenseless, acts that most people would find abhorrent.
Student or Learner