Did the IDF shoot people from the helicopter?

One of the more consistent stories from the interviews of people aboard the Mavi Marmara is that the IDF started shooting and killing them from the helicopters in the air. For example, from an Al Jazeera reporter on the ship:

Two helicopters at a time hovered above the vessel. Commandos on board the choppers joined the firing, using live ammunition, before any of the soldiers had descended onto the ship.

Two unarmed civilians were killed just metres away from me. Dozens of unarmed civilians were injured right before my eyes.

One Israeli soldier, armed with a large automatic gun and a side pistol, was overpowered by several passengers. They disarmed him. They did not use his weapons or fire them; instead they threw his weapons over board and into the sea.

There have been other reports that made the same accusation.

However, no one was killed from the helicopters.

First of all, if there was really shooting from the choppers, it seems highly unlikely that the IHH thugs would be hanging around on deck like sitting ducks.

Moreover, Turkish forensics reports indicate that all the people killed had 9mm gunshot wounds. I am no gun expert, but a 9mm gun has a limited range and does not seem to be a weapon that could be used with any effectiveness from a helicopter.

The idea that the IDF would send soldiers into an already-existing combat situation - shooting live ammo at the people on deck - while armed with paintball guns is beyond absurd.

Every video I've seen - of the IDF soldiers on the deck and in the boats alongside the ship - show them with paintball guns, not submachine guns or other large lethal weapons.

And one thing is very clear: the witnesses on the ship did not know the difference between paintball guns and large automatic weapons. 

 Paintball guns have a much wider barrel than ordinary submachine guns, and I can imagine that those guns look terrifying to people, especially since there was so much confusion and the sight of the rappelling soldiers were probably accompanied by non-lethal percussion grenades making loud noises, not to mention the noise of the choppers themselves.  There is also no doubt that seeing a paintball gun being shot in such circumstances would also be disorienting - especially if the pellets were of red paint.

This could explain a lot of the discrepancies between the witnesses and the videos/IDF/soldier testimonies. Combine the confusion with the certainty that the activists have to assume that Israel is inherently bloodthirsty and you have the ingredients for highly inaccurate "eyewitness" testimonies. (Other statements, such as the Free Gaza claims that the IDF was shooting people in their sleep or that there was no resistance by the Mavi Marmara people, are absurd on the face of it and have been quietly dropped, although never corrected.)