The appearance of a threat to all of the people convinces Gideon to spare Noah’s life. What Noah does with that life is to demonstrate the division that existed among the people. Gideon would begin to work to defend the people. Noah ordered the people to flee with their women and children.
Mormon doesn’t tell us what is behind this exodus. Clearly Noah fears that the people would be killed, including women and children. Perhaps it was another invasion such as had caused the people of Mosiah (father of Benjamin) to leave the city of Nephi. Linguistic and archaeological evidence from that time suggest that the elites of the region were dispersed. If that were the fear, it would explain why it was the elites of the city who fled.