The ship was in international waters, whether the protesters were peaceful or not boarding the ship was tantamount to piracy.
Yes, but they took it in international waters for a justifiable reason (in security terms at least), and one which would probably hold up in court. The large size of the flotilla meant that had they waited until the ships reached 'Israeli' waters, they might have slipped through if things didn't go according to plan (which they didn't). It is my understanding (and I could ne wrong) that in such situations, action in international waters is legitimate.
Even if they were attacked, the ship was boarded illegally by armed men.
Do you know that it was illegal? Although I have seen lots of reports point out that it took place in international waters, I have yet to see any legitimate sources claim that it was an illegal action. To my knowledge it is more complex than you suggest.
If the police were to break into somebody's home illegally, then (after being attacked), end up shooting and killing several of the family members, should the police be able to claim self defense?
The question of legality looms large in this, and until that is settled I guess this isn't going anywhere. My main point is that the organisations behind this protest action spent much of yesterday claiming their actions were entirely peaceful and that they did not initiate the violence, something which has been shown to be totally untrue.
This was a botched operation, yes, but it was not a peaceful protest, and the instant you use potentially lethal violence against soldiers (as the 'lynch mobs' seen in the footage certainly appear to do), or take and brandish firearms (as per eye-witness accounts), you're asking for trouble.
Israel has to be held responsible, because ultimately if you initiate such an assault, you are responsible for its outcome. Their goal was to pacify the protesters and seize control of the ship quickly and without incident; the loss of life represents a massive failure on the part of the people in command. However, the protesters claimed to be peaceful, and effectively sailed under the white flag. Their actions show that they were at best disingenuous, and at worst reckless and irresponsible. Who's going to believe that the next convoy is filled only with peaceful protesters?