I think it was named by the Spanish Conquistadors who were conquering that area. It's original name was Provincia De Nuestro Señor Jesucristo El Salvador Del Mundo, but they changed it to El Salvador. I might be wrong, but that is all I know. !
The Conquistadors wore better armor than the Inca and Aztec. Also the Conquistadors rode horses which neither the Inca or Aztec had seen before, so that added a psychological advantage to the Conquistadors. In addition to that, the Conquistadors had gunpowder.