In the cable, dated Sept. 16, 1976, Kissinger rejected delivering a proposed warning to the government of Uruguay about Condor operations and ordered that “no further action be taken on this matter” by the State Department.

My reading of this is that the cancelled note was intended only for Uruguay and not for Chile, which we now know was directly responsible for the Letelier hit. The situation in Uruguay at the time is highly relevant.
President Juan Bordaberry, who had been installed in a military coup in 1973, had been removed in June, 3 months before the Kissinger action. It was Bordaberry who had created a notorious torture regime in Uruguay. He was replaced by the elderly and much more moderate Alberto Demicheli, who favored a partial restoration of civil rights. Demicheli, in turn, was replaced by Aparicio Mndez in early September. It was Mendez who supervised the return to democracy, with a Constitutional referendum in 1980. This resulted in the defeat of the military regime’s program and a return to democracy.
In light of these events, and the changes taking place at the time, it is likely that Kissinger decided the warning was not necessary for Uruguay, which had already taken steps to moderate its policies.

As a postscript, Bordaberry was arrested on November 17th 2006 and charged with involvement in the assasinations of two exiled legilators, Zelmar Micheliniand Hctor Gutirrez and in Argentina in May, 1976. He was convicted and sentenced to 30 years. He is now 81 years old and is in poor health.