An actual Mossad agent responds
European intelligence agencies, angry at their own governments' temerity in the face of Arab intimidation, generally looked the other way when a Palestinian terrorist was eliminated on their soil [...]
I know of no case in which a Mossad operative had a crisis of conscience about these operations, which were understood to have the clear and immediate purpose of saving innocent lives. When I inquired, at an early stage, as to the nature of the quasi-judicial mechanism invoked back in Tel Aviv to determine the guilt of targets for assassination, I received a clear and convincing response. Needless to say, targets were determined and located through an extensive intelligence-gathering operation by Israelis, and not in the dubious way depicted in the film [...]
During the 1970s, none of us had qualms about "moral equivalency", an issue debated by the Israeli characters in Munich. Palestinian terrorists were killing innocent civilians; in response, Israel was targeting only terrorists and the terrorist infrastructure. When a single nonterrorist was killed by mistake [...], the entire operation was closed down.