If a boy is about to seriously hurt another boy and we just stand there looking and let it happen, when we could have easily stopped it, we will surely be condemned, even by the secular authorities, so how can God do the exact same thing and still be good?
1. God allows free will, for both good and evil.
--In your example, even if the first boy was stopped from harming the 2nd boy, the first boy sinned by anger/hate. The sin is separate from the human act of inflicting harm.
2. God has delegated to man to duty and authority to have dominion over the earth. It is man's job to take care of earthly affairs, to the extent of our ability. When things are beyond our control, then we pray for His intercession.
--In your example, it is the duty of any adult to step in correct the first boy for his anger/hate. God also corrects the boy, through his conscious and by the guilt he feels for sin, and by the inspirations he receives from the Holy Ghost and his guardian angel. God gives to all men a conscious and a guardian angel as a guide through life. But neither God, nor angel, nor any person on earth can stop a boy from sinning because all men have free will.
It would also be the duty of any adult/supervisor to stop abuse/fighting between boys. However, the fighting/pain inflicted is not a sin; the anger/hatred is the sin. The pain felt by the 2nd boy who was beaten up is a penance that God allowed to happen and is not sinful. If God allows suffering in our life, this is typically a blessing (so we can avoid purgatory) though our human nature needs spiritual education to understand this.