Dozens of air force officials will also face disciplinary action, including for trying to cover up the case.
It had sparked a public outcry and the air force chief resigned in June.
Separately, a court ruled the military had unlawfully discriminated against a transgender soldier who was forced to quit and was later found dead at home.
The cause of death of Byun Hee-soo, South Korea's first transgender soldier, has not officially been given but it is reported she took her own life.