He was persecuted – Ele foi perseguido (politicamente, religiosamente, ou por questoes de etnia, raça, etc)
He was prosecuted – Ele foi acusado… (legalmente por uma corte de justica)
Persecution is the systematic mistreatment of an individual or group by another group. The most common forms are religious persecution, ethnic persecution, and political persecution, though there is naturally some overlap between these terms. The inflicting of suffering, harassment, isolation, imprisonment, fear, or pain are all factors that may establish persecution. Even so, not all suffering will necessarily establish persecution. The suffering experienced by the victim must be sufficiently severe. The threshold level of severity has been a source of much debate (definicao da Wikipedia)
Prosecution: The institution and conducting of legal proceedings against someone in respect of a criminal charge.
The party instituting or conducting legal proceedings against someone in a lawsuit.
Institute legal proceedings in respect of (a claim or offense): “the state’s attorney’s office decided this was a case worth prosecuting”