Whether he knew they would be killed or not I'm very skeptical that he was
shocked by it. The fact that Lodge refused to intervene - was a passive
spectator - indicates to me that it apparently wasn't much of a concern.
Maxwell Taylor, the then Chairman of JCS who would later be named
ambassador to South Vietnam by LBJ, said this about the coup: "There was
the memory of Diệm to haunt those of us who were aware of the
circumstances of his downfall. By our complicity, we Americans were
responsible for the plight in which the South Vietnamese found
themselves".
As Colin Powell said about Iraq, "If you break it you own it." Once JFK
"broke" the government our involvement deepened considerably - morally,
politically, militarily. This situation what LBJ inherited. He gets blamed
for almost all of it while JFK gets a pass. History isn't fair but neither
is life.