CIA operations in the 1950s can be said to have harmed American foreign relations in the long term.  This was particularly true, one can argue, with respect to places like Iran and Latin America where CIA operations overthrew or tried to overthrow governments that were at least somewhat popular.

The most obvious example of this can be seen in Iran.  In the 1950s, the CIA participated in a coup in htat country.  The CIA helped to arrange for the overthrow of Mohammed Mosaddeq, who was the prime minister of the country.  The US felt that Mosaddeq was excessively influenced by communism or that he was himself a communist.  Because of this, the CIA helped to overthrow him.  This hampered US relations with Iran, in the long term.  The fact that the CIA did this and installed the Shah helped to bring about the Iranian Revolution of 1979 and the current tensions between the US and Iran.

Similar things happened in Central America.  US interventions in that region (such as the overthrow of Jacobo Arbenz in Guatemala) helped to cause countries in the region to see the US as something of an imperial power.

In these cases and others, CIA actions in the 1950s made enemies for the US, making its foreign relations difficult in the long term.