Let me summarize my thoughts: the raid shouldn't have happened in the first place. That was IDF's mistake. But since it did, I'm giving a lot of blame on the activitists on the ship. When you're dealing with special forces, a Gandhian approach is highly advisable. Let me repeat that: if you are dealing with a bunch of elite soldiers armed to the teeth, you should do this: a) duck for cover and b) offer passive resistance at the most.
The activists had prepared themselves for the raid. You could claim that the iron bars were improvised weapons one grabbed on the spur of the moment, but that doesn't fly when we talk stun grenades, slingshots and pepper spray. Also, if you walk around with a big metal bar and throw something at a IDF commando, don't be surprised if you get a bullet in the head. More on that later.
Have a look at the IDF footage. Even if the soldiers interviewed were lying and evidence planted, you got some scary images.
In particular, look at those two:
On the IDF side, you have to wonder who's the guy/girl who coordinated the assault. Did they sleep during their strategy class? The IDF ships approaching the vessel were thrown stuff at, including stun grenades. Don't get surprised when some of your commandos get attacked BEFORE they even finish reaching down. I'm no military commander, but I think this situation demanded a LOT of flashbangs before you put any of your commandos down.
And I'm not the only one thinking along those lines:
Some people were accusing the IDF of sending grenades first. I haven't seen that. Maybe I just haven't seen the right video. If that is true, that's a pretty gross human rights violation right there. But I doubt they did that, because I have problems believing that a bunch of guys would be patiently waiting for commandos to come down the ropes to beat them if they just had received a few grenades their way. We're talking about a ~15m antipersonnel blast radius here.
The biggest DOH here: why did they even raid in the first place? They were in international waters, and they were underwhelmed... Can't you wait until the ship reaches territorial waters and wait for it with a much bigger force?
I am an armchair analyst, so take my word for what its worth... Now, for the other armchair analysts who are bound to criticize me: don't come up with this slingshots vs bullets argument. First, because I know for a fact that you can use a slingshot with metal balls to hunt small animals (my dad has that equipment), so that's a real threat. Second, because we are talking about a combat situation with microsecond reaction time: nobody has time to do any threat analysis. If you're attacking a commando, expect a bullet back. Consider yourself lucky if you got a kick in the gut or a rifle's stock in the face.
It looks to me like both sides wanted a fight, and they got it. Shame on IDF for assaulting a ship in international waters. Shame on the minority of crazy activists who transformed their vessel in a small warzone.