What exactly happened when Israeli commandos took over the Pro-Gaza activists' boats is still murky. It is now clear that there are some deaths, though the number is quite uncertain, as reports range from 2 to 16. Israeli reports say the soldiers were attacked with clubs and knives and some activists tried to take over the soldiers' guns. That definitely contributed to the death toll.
Nobody is blameless in this fiasco. Israel's policy on the matter was ill advised from the beginning. The navy should have just allowed the boats to reach Gaza after an inspection of the cargo for weapons, though right now I'm not sure whether or not the provocation-seeking activists would have peacefully let the navy on board for such inspections.
The activists, on their part, wanted to make Israel look bad more than they wanted to bring aid to Gazans or to "break the siege". They claimed they come in peace and that they would not violently resist, but resist they did. Pictures coming via Turkish television show activists attacking soldiers with clubs. They didn't actually think they could win, repell the Israelis and then reach their destination. At least some of the activists, if not most of them, wanted there to be a riot to make Israel look as bad as possible.
If anything good will come of this terrible situation it will be that nobody but crazy people with suicidal tendencies will want to come on these publicity stunt boat rides, bringing aid that, for the most part, comes in via the Israel-Gaza border anyway.