What did priates do to their prisoner?

Answer 1

Flogging. This treatment was universally popular at the time, on and off the high seas.

Man Overboard. While this could be as simple as merely tossing the captive or prisoner overboard, it was sometimes varied to relieve the boredom of a long trip. Sometimes a man would be tied to one end of a rope and dragged until he died from drowning or exhaustion. Perhaps this was how water skiing was invented.

Dunking. This was less popular, as it required dunking the prisoner then hoisting him back up again, suspending him for hours above the water. It was too time-consuming, and aside from the initial spluttering and choking, not that entertaining.

Marooning. This was the most common form of punishment for serious offenses like desertion. A sailor was either placed on a raft or left on a deserted island to die. If left in the water, he was often mercifully given a pistol to kill himself before the sharks got him.