The ship was in international waters and clearly not a warship. That orders to move away given in an abundance of caution didn’t arrive in time has no bearing on the situation. It should not have been attacked for that reason alone. Pilots were clearly able to identify the ship as there are several recorded exchanges in Israeli headquarters about it being an American ship before it was attacked and visual contact with pilots was their only contact with Israeli forces until they were attacked. So even the attacking pilots should have known. The only reason they would attack anyways is if they had direct orders to fire, with that knowledge. In fact in one of the recordings they bring up the American ship and are ordered to fire anyways.
Once there was an attempt at communication, the response was ignored and they were torpedoed anyways.
There’s no way to interpret this as anything other than a brazen and willing war crime to neutralize an American ship.