Well, the early 70's were a terrible time for the cause of Freedom in the world. The communists were on the march all over the world, and South America was looking good for them. Pinochet was not neccessarily the obvious choice to lead the coup. He led the coup because where other generals demurred in the face trouble, afraid of course of the consequences, Pinochet stood up to be counted because he did not want to see Chile and South America fall to the communists. And it's not like Pinochet did this on a whim, he ahd the support of both the congress and the supreme court.
After he won, he instituted sweeping free-market reforms, creating a retirment system that we ought to emulate. Later, when the communist threat was gone, he voluntarily stepped down and held free elections. Who knows what South America would look like if not for Piochet? Who knows whether or not hte Soviet Union would have collapsed had all of South America gone communist? Yes, some communists were killed by the government. It was war. You cannot expect a fragile government to stand idly by while communists financed by Cuba and the Soviet Union attempt to topple it and replace it with a communist dictatorship. If freedom is a natural right, then those who attempt to take away freedom by foreign financed insurrection should expect to be treated as foregin soldiers committing an act of war.
What is needed today is more leaders like Pinochet in Brazil and Venezuela.