Why did Frank Castle save the kid during the robbery?

The earlier conversation between "Pete" (Frank Castle/the Punisher's alias) and Donny established that Donny is working to support his family, in particular his grandmother.

Frank has also experienced workplace bullying at the hands of the other labourers, due to his deliberate antisocial behaviour and an implied disapproval of their workmanship and work ethic.

Frank later overhears the plot to rob the gangsters, and naturally pieces together an overview of the events at the restaurant.

Upon seeing the group about to kill Donny as a cover-up, his first reaction is that Donny is innocent and the group needs to be handled. This being the Punisher, "handling them" is a predictable scene.

Frank/Punisher doesn't have moral qualms about robbing criminal gangs (as seen in later episodes), nor about generally ending their existence (as seen at the start of the episode). Donny's motive is also an honourable one: to care for his family. Frank has a very high regard for the integrity of family. As the loss of his own family and the devastation to his life is his own motive for originally becoming the Punisher, he is likely to sympathise with Donny's position.

Therefore, these actions are entirely within character for Frank/Punisher, and serve to reinforce the nature of his character shown in later, more complex scenes and subplots.