The peace activists were armed?
At :24, you can see an Israeli soldier being beaten with what appears to be an iron bar (the propaganda convoy was carrrying construction materials among other things.)
IDF: Gaza flotilla activists stole 2 handguns from soldiers
It's an old trick: Confront armed security forces with a murderous mob armed with improvised weapons (iron bars, boards, etc), then scream bloody murder when the security force use firearms to keep from being beaten or hacked to death. Many a soldier and policeman has been killed and mutilated over the years by mobs of savages because he hesitated to use gunfire to defend himself. Lethal force does not require guns and bombs, but it does merit a lethal response.
A case in point from Northern Ireland
According to the BBC, there were 600 people aboard the ship that was boarded. A mob that size could easily overwhelm a small boarding party if the latter refused to use their weapons, something the "activists" and their media shills were probably counting on.