Genocide is a loaded term and in the last sentence here he says "plans are being made and programs implemented on the assumption that they may lead to the death of several million people in the next few months."
Again: he was accusing the government of planning genocide. The most likely explanation of why it didn't happen is that they weren't making plans and implementing programs for a silent genocide. Seeing as how they trounced the Taliban, if they had wanted a silent genocide they would have gotten one. The Secretary of State of a Republican administration and former cold warrior just admited that the September 11, 1973, US backing of the coup in Chile was an error and that the US isn't proud of it. Surely Chomsky can admit a mistaken analysis.
Peter