The Israeli soldiers were protecting themselves. I believe they were doing the best that they could during the attack to try to stay alive. Some people claim that warning shots would have been enough. However, when you are in a fight, sometimes screaming stop just does not do anything to the person that is attacking you.
There was no excuse for Israeli troops to raid the ships. The flotilla didn't open fire on the Israeli Navy and passengers only defended themselves after troops bruised and bloodied them, killing nine civilians along the way. If Israel was that scared of aid ships going to Gaza, warning shots should have sufficed. Sink the ships slowly, evacuate the passengers and then deport them. Don't board the ships first and start violence.