how a moral army should be investigated

Maybe there is not a single moral army in the world. More than likely, after all, the two concepts seem to kind of cancel each other out, but there are international laws that govern the rules of engagement, and recently a U.S. soldier was imprisoned for 35 years for the murder of prisoners in Iraq. This seems to be the kind of investigation that should be held into soldiers' actions, not the whitewash that promises an investigation, but never delivers, and which protects its members from investigation, or which only investigates them if there is more than enough of a public outcry, and even then, which often gives lenient or no sentences for crimes committed* (see end of this post). Spain is investigating crimes against humanity that it is alleged Israel committed in Palestine in 2002. The reason why Spain decided to pursue the investigation is due to the fact that Israel was not investigating it. B'tselem, the Israeli human rights watch, and other human rights groups issued this press release on the 19th of March, this year:

Circumstances point to the inadequacy of internal military investigations. The Military Advocate General only ordered the opening of an investigation by the Military Criminal Investigation Division following the publication of the Haaretz story, three weeks after the relevant materials reached the Chief of the General Staff. This tardiness follows a pattern of failures to investigate suspicions of serious crimes and illegitimate officer orders. Such partial investigation represents only a fraction of the necessary attention into this matter and raises suspicions that the norms of whitewashing serious crimes have spread across all ranks of the army. Read more.

Indeed, this infamous video from 2008 of a soldier shooting a handcuffed, blindfolded Palestinian detainee in the foot - was the only reason that the soldier supposedly got investigated. Strangely enough, it made it to international the news. I remember reading about it at the time. From B'Tselem:

According to press reports, the Military Police have opened an investigation and arrested the soldier who fired the shot. Apparently, until the video was aired, the army did not conduct a Military Police investigation, and settled for an operational debriefing. According to the reports, the debriefing reached the desk of the Judea and Samaria (West Bank) Division Commander, who failed to inform the Military Police or the Judge Advocate General’s Office, or to take any measures against the soldier or the battalion commander. Residents of Ni’lin stated that, the day after the incident, they saw the soldier still serving in his unit.

I haven't read of any follow up. Maybe the fact that the Israeli Ministry of Justice lawyers have said:

“The State of Israel is at war with the Palestinian people, people against people, collective against collective”,

justifies every and all actions, though as stated at the beginning, democracies and signatories to the Geneva conventions and so on, surely have rules of engagement, particularly pertaining to civilians. Again, from B'Tselem:

... it is not correct to define the situation in the Occupied Territories as armed conflict. Some of the actions taking place in the Occupied Territories are indeed combat actions, but a significant number of IDF actions - at checkpoints, in dispersing demonstrations in which the Palestinian side does not open fire, in arresting Palestinians - are normal police actions of the kind that were carried out by soldiers in the first intifada. Furthermore, even if the situation is one of armed conflict, the army is still required to investigate attacks on civilians. Armed conflict, too, has rules, and intentional attacks on the civilian population are forbidden. To ensure that soldiers comply with these rules, such incidents must be investigated.

If you look at Alison Weir's video below, Off the charts, even before this Gaza offensive, the number of Palestinian children who died, or have been injured (losing eyes, shots to the head) is unbelievable and tragic, even in so called peace times.

The soldiers' testimonies from recent Ha'aretz articles which have been supported by human rights reports, Palestinian reports and AP reports, have been "debunked" in both the States, the blogosphere, and in elements of Israel as "hearsay", accusations of blood libel being thrown out - more likely heresy in that someone is speaking the truth. So why not investigate it, rather than throwing PR into full spin, and smearing everyone who speaks out? What is there to hide?

As an endnote, the sentences handed out to settlers who murder Palestinians are laughable, also.

...[E]mergency laws ... allow Israeli civilians residing outside sovereign state territory to be tried in Israeli courts under the purview of Israeli criminal law. In contrast, Palestinian citizens are tried in military tribunals that use a different set of laws and punishments.

As such, a settler may be released on bail and given probation for a crime that would land a Palestinian in custody until the end of legal proceedings, followed by a long prison sentence. Prior proposals to transfer some cases of crimes by settlers to military court jurisdiction were rejected under defense establishment pressure.

*And this from a 2007 US Department of State report, Bureau of Democracy, Human Rights, and Labor, (which also details abuses committed by the western-backed Palestinian authority, and Palestinians), part of which details the [lack of] action taken against police and soldiers in the occupied territories when they commit crimes, or within Israel itself, so the same kind of leniency will be shown to the soldiers who fought in Gaza, I expect:

On January 19, a border policeman killed Nadim Milham, an Israeli Arab, while reportedly searching for weapons in his home. A family member reported that police beat Milham and shot him when he attempted to escape; the Mossawa Advocacy Center for Arab Citizens of Israel (Mossawa) claimed to have evidence that Milham was shot twice from behind. On November 21, the State Prosecutor's Office indicted the policeman for manslaughter; however, there was no further action by year's end.
...
On August 11, an Israeli Border Police soldier fired a rubber bullet at the head of Lymor Goldstein, an Israeli demonstrator protesting construction of the separation barrier in the West Bank village of Bil'in, injuring him and requiring surgery to remove the bullet. No action was taken against the police.
...
There were no developments in the September 2005 case in which IDF soldiers forced residents of a home in Tulkarm to undress in the street or the November 2005 report that IDF soldiers assaulted Palestinian students in Hebron.

There are many more stories and much more information in the report.