One source I can link to, however, is a Palestinian blogger who is relating the story of one of the passengers, Shatha Barakat. The blogger is definitely an interested party, so take this with a large grain of salt, but I'll repeat it anyway. These stories need to be collated and recorded.
According to Flotilla passenger Shatha Barakat, Syrian national and one of the detainees who was released from the Ber Al-Saba, in hebrew Beer Sheva jail, "when I went to the top of the ship to help the sanitary unit to take care of the wounded people, I saw the commandos landing during heavy shooting toward our ship from the Israeli boots surrounding us and also from the helicopters". She confirmed that some Israeli soldiers were wounded on board the ship due to the indiscriminate shooting by the Israeli military helicopters and boats (friendly fire). She stated that all peace activists were unarmed and that nobody was carrying any kind or weapon.These are possibilities I hadn't considered. I had thought that the shootings were due to panicked, frustrated commandos who had completely tossed out their ROEs, and that the injured commandos were really shot. That there might have been deliberate hits, and that the injuries were friendly fire, was not even a possibility in my mind.
Neither may be true, of course. But it's another reason why the IDF might have been so desperate to shut down independent records of the event.