Set aside the matter that stealing cabinets of documents cannot easily be construed as a refusal to be immoral. Set aside also the fact that even with the documents as published by Haaretz, it's hard to see what illegal actions might have happened on which she was allegedly reporting. Set aside the fact that the Attorney General looked into the matter, just in case, and found that the "crimes" Uri Blau was alleging didn't happen, and the army acted according to the law. (Link here, relevant paragraph only in Hebrew: interesting, isn't it).
Setting aside all that, there's still the principle whereby a soldier must obey orders, but sometimes a soldier may not obey orders. Israel worked out this conundrum back in the 1950s. I wrote about this in Right to Exsit, and am reproducing the relevant page or two here (p. 123-124):
Israel’s second war, the Sinai Campaign, began on October 29, 1956. On the first afternoon, fearing that the war might spill over to the Jordanian front, an order was given to harshly enforce a curfew in the Israeli-Arab towns along the Jordanian border. The commander of one of the units of the Border Police, stationed at the town of Kfar Kassem, interpreted this in an extreme manner, and his troops shot 47 villagers in cold blood – workers returning from work without having heard about the curfew. It was a cold-blooded murder of innocent villagers, with no alleviating circumstances.
This time the killers were put on trial; two of the commanding officers were sentenced to many years prison, although they were later pardoned, and this pardon was a blot on Israel’s record. The long-term significance of the case, however, was in its legal and educational import. Henceforth Israeli soldiers were told that it was their legally binding duty to disobey what were called “categorically illegal orders.”
Categorically illegal orders are a modern version of the sixth commandment, “Thou shalt not murder.” Soldiers are expressly forbidden to murder, even if ordered to do so on the field of battle; if they do, they will be court-martialled. The order they were given will not be relevant to their defense, since their moral duty as human beings supercedes their duty as soldiers. Such a ruling can be applied only rarely: a merely “illegal order” must be obeyed; the “categorically illegal orders” must be disobeyed. The definition given by the court was hardly helpful, unless you came from a tradition that had been using the distinction between killing and murder for three thousand years: a categorically illegal act is one above which a black flag flutters.
With such a literary metaphor, 18 and 20-year-old youths are armed and sent to battle. They must obey the orders of their commanders, under threat of court-martial, because otherwise an army cannot function; but they must not obey when they see the black flag, under threat of court-martial, because otherwise the society they defend with their lives may not be worthy of the sacrifice. This is the Israeli definition of Jus in Bello. It is not a philosophical construct for academic seminars but a component of training for battle. Israel’s record prior to the murders at Kfar Kassem hadn’t been bad; it was generally to improve from here on. The cold-blooded lining up of civilians to be shot has never repeated itself.