Prosecutors allege he molested a 12-year-old boy for two years more than a decade ago.
Emami says there were concerns that Stenger was a suicide risk and his case file was sealed to prevent him from knowing of his pending arrest.
Stenger's body was found Wednesday afternoon in the driver's seat of the patrol car in an Aliso Viejo shopping center parking lot. He had a single gunshot wound to the head.