I'm confused.
Does or does not the movie show Israeli soldiers taken down, beaten by group of men with blunt objects, stabbed and thrown overboard?
Does or does not the attachment to this post also proves the existence of knives and bats on board - presumably the same ones actually used against the soldiers?
Were four other ships been boarded successfully under the same conditions, with the hundreds of people aboard them acting calmly and avoiding any confrontation?
And what on earth would you do if you were lying on the floor being beaten by five men with blunt objects or if your friend was thrown from a 10 meters (that's 30 feet for you) height?
As far as I'm concerned it's very simple:
A state has decided to board a vessel approaching it's waters. The legality of this issue is marginal and it's a waste of time to focus on it (for the record, it was legal

).
Four ships were boarded without casualties.
On one ship, a large group of people attacked the commandos in close quarters, overpowering some of them, beating them up, stabbing them and causing life threatening injuries.
At that point the commandos did what any sane man would do and defended themselves. At close quarters knives kill just as well as bullets.
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And if you're confused by so much text, I'll leave with a final thought:
Who in their right mind assaults IDF soldiers in the middle of the night with knives and bats and expects not to get shot in return?! Think about it for a moment. Forget all the background, it's irrelevant. YOU DO NOT ASSAULT ARMED SOLDIERS WITH COLD WEAPONS. YOU RAISE YOUR HANDS AND DO WHAT YOU ARE TOLD.
No matter the circumstances, if someone raises a knife at me and I'm armed, I might consider shooting for the legs... If everything around is in chaos, you might as well expect one between the eyes.