Once you storm a ship in international waters, regardless of what happends to you, you have no right to claim self defence. You are the agressor, the attacker, not the one defending youself from an attack. The people on the flotilla acted in self defence against your agression and had every right to do so.
Turkish military denies hitting civilians in airstrikes targeting PKK militants (Reuters)
from the article: Video: Gaza flotilla activists attacking Israel Navy commandos