Deborah Leonard did not feel she could stand up to other members of the Word of Life church in New York state, said her lawyer, Devin Garramone.
Her son Lucas, 19, died from the attack and his brother is in hospital.
Police say they were beaten by Mrs Leonard, her husband and five others in order for them to confess their sins.
All six people arrested, including the boy's father and sister, have denied the charges.
"It looks like she went along with it, and it spun out of control," said Mr Garramone, who described the incident as an "intervention".
"This woman is so meek and timid, she didn't have the temerity to stand up to them and say, 'You're not punishing my kid. You're not doing this.'"
Some of the others arrested may have caused the fatal injuries, he said.
The boys were repeatedly kicked and punched on Sunday but it's not clear why.
Police have described the beating as a "spiritual counselling session to urge [the boys] to confess sins and seek forgiveness".
Ms Leonard's husband Bruce, who founded the secretive church in New Hartford, New York, said it was a family meeting that had nothing to do with the church.
Lucas died on Monday morning in hospital, where his parents took him the morning after the attack.
His 17-year-old brother Christopher remains there in a serious condition.
The parents have pleaded not guilty to manslaughter and the other four have pleaded not guilty to assault.
The Word of Life church is nearly 30 years old and its membership has fallen in recent years from about 40 to 20, said a local police chief. Some live at the church.
The church refused help from firefighters when the building caught fire a few years ago, he said.
A woman charged with beating her son to death in a church has said she "felt helpless" to prevent the violence committed by other church members.