The reason given by Barak is this: "Barak fears that soldiers will be reluctant to carry out missions if an inquiry panel can later penalize them for anything that goes wrong." !!!! That argument is pure bullshit: no army asks for a vote from the soldiers before ordering them into action, so their "reluctance" about those orders is immaterial i.e. you either carry out your orders or you face a courts martial.
Police disperse hundreds in brawl in Kafr Manda, northern Israel (Haaretz)
from the article: Despite wider remit, soldiers won't be questioned in Gaza flotilla probe