I don't remember Reagan ever saying they were our 'best friends'. He was just choosing the lesser of two evils. He knew that the 'right wing' in El Salvador was fighting a real war against Communists who were being supported by the Soviet Union, and he decided to use them to fight the left wing. Yes, atrocities like the murder of the nuns were committed, but Reagan was right to support the right wing. It helped slow the spread of Communism in Central America.
Of course in his big 1984 convention speech Mario Cuomo made reference to Reagan's friends killing these women, and implied it happened on Reagan's watch. In fact, the killings occurred in Dec 1980 when "St" Jimmy Carter was president.