In fact, the IDF's Military Advocate General and the MAG Corps are completely independent. They do not report to the IDF structure; rather they report to the government directly. The leader is appointed by the Minister of Defense.
As the MAG webpage describes him:
As the State of Israel's report on Cast Lead put it:
The Military Advocate General is a member of the General Staff, but has complete legal independence and is not subject to the direct orders of the Chief of Staff or other superior officers.
The Military Advocate General is appointed by the Minister of Defense on the recommendation of the Chief of Staff.
The decisions and legal opinions of the Military Advocate General are considered determinative in all areas relating to law and the military and must be adhered to by all bodies of the military.
IDF military lawyers were involved in advising commanders on international law aspects of the Gaza Operation. The IDF structure ensures that the IDF legal advisors can provide frank and professional advice. All legal advisers belong to the MAG Corps and are not subordinate to the commanders they advise. According to Israeli law, the head of legal services in the IDF, the Military Advocate General has an independent status outside the military hierarchy in relation to all legal issues. In principal legal aspects the MAG is subject to the guidance and supervision of Israel’s Attorney-General and regularly consults with the Attorney General. In addition, IDF activities, including during active combat, as well as all MAG and Attorney General decisions are subject to judicial scrutiny and review by Israel’s Supreme Court sitting as the High Court of Justice. As discussed below in Section V.C(5)(c), the High Court of Justice regularly reviews such activities and decisions, and intervenes in appropriate cases.It is worth noting that the MAG Corps was established as a completely independent entity some 55 years ago.
...Israel’s legal and judicial apparatus is fully equipped and motivated to address alleged violations of national or international law by its commanders and soldiers. Such allegations are reviewed through a multi-tiered system of independent and impartial proceedings before Israeli investigative, administrative and judicial authorities, including Israel’s highest judicial instance, the Israeli Supreme Court.
Israel has a military justice system that operates within the IDF but is professionally independent. The military justice system is based primarily on the Military Justice Law of 1955, a comprehensive statute which governs the investigation of misconduct and indictment and prosecution of offenders and establishes the Court Martial system. The military justice system empowers the Military Advocate General to try soldiers not only for unique “military” offences (such as absence without leave, conduct unbecoming an officer, etc), but also for ordinary criminal offences under Israel’s Penal Law, 1973. Any and all allegations regarding offences committed by IDF personnel, and related to the military, are dealt with through this multi-tiered system, including allegations regarding improper conduct on the battlefield.
The IDF system of review includes three main components: the Military Police Criminal Investigation Division (“MPCID”), the Military Advocate General’s Corps (“MAG”), and the Military Courts. The MAG Corps and Military Courts are both independent from the IDF command hierarchy, are subject only to the law, and are also entirely independent from one another.
A number of years ago, anti-Israel activists tried to get Spanish courts to prosecute Israelis for actions that occurred in Gaza, under Spain’s Universal Jurisdiction statute, using the argument that the internal IDF judicial system cannot investigate the IDF indpendently. Last summer, the Criminal Chamber of the National Court of Spain threw the case out. As the Cast Lead report mentions:
The Criminal Chamber of the National Court of Spain emphasised Israel’s ability to fully and fairly investigate the charges itself. It held that Israeli procedures and decisions with regard to the legality of preventive strikes under international law, and the military, civilian and judicial review in Israel of the Shehadeh incident, comport with the principle of complementarity, as the State of Israel is a democratic country where the rule of law applies.The group that created the rebuttal to the Goldstone Report due out this week is headed by a former IDF chief intelligence officer and the MAG was a part of the task force he led to help ensure independence in the project.