Since those on board the ship were supporting a terrorist organization dedicated to Israel's destruction, they lost their civilian status. If you wish to call them civilians, then you must agree that Hamas, the IHH, and Turkey were using them as human shields. Israel had every right to do what it did to prevent this group providing materials to Gaza, or, if that was really their aim, and you have to be exceptionally naive to believe that, they could have transferred them, as requested, via Israel.
Donald Trump: Israeli settlement construction in West Bank should 'keep going' (Haaretz)
from the article: Operation Mini Cast Lead