The Guardian article from 2003 about the Nirim Affair I think shows several significant things.
Quoting :
He and most of the soldiers at the outpost were tried in secret. Some said they were carrying out their commander's orders. The military judges rejected that line of defence. Moshe denied rape. "Morally speaking, it was impossible to sleep with such a dirty girl," he told the court.
(This shows clear dehumanisation of civilians on the part of this group of soldiers : the fact that they were tried in secret does ALSO show that at the height of the war there were Israelis willing to stand up for human decency against their own soldiers. The most danger is when a country cannot do this. The question remains to what extent, if any, war crimes were encouraged from higher up).
He was acquitted of rape but convicted of murder and sentenced to 15 years in prison. The judges likened his stated willingness "to murder even women and children in cold blood" to "Hitler's methods in France".
Nineteen other soldiers received light sentences of between one and three years, mostly for "negligence in preventing a crime".
(So the judges at least have strong condemnation. Why the light sentences?? This is of course, in context, sadly not unique . Wartime sexual violence was hushed up and taboo by all kinds of armies until recently).
The appeal court reduced their sentences, saying: "At the time there was a general feeling of contempt for the life of Arabs ... and sometimes wanton events occurred in this sphere. All this helped create an atmosphere of 'anything goes'."We are convinced that this atmosphere existed at the Nirim outpost, too."
(So the appeal court themselves admitted that there was a 'general feeling of contempt for the life of Arabs'. Very disturbing.
At the same time, I've read a lot of accounts that DO show soldiers then avoiding harming civilians. Clearly most soldiers did NOT behave the way the soldiers in Nirim & other atrocities did.
The fact 'general feeling of contempt' was used to justify lighter sentences makes me wonder if they were arguably to some extent unfairly condemning the army as a whole when plenty of soldiers did NOT succumb to this 'general feeling', so as to try and get these men lighter sentences.)