The shots fired probably after the filming, or the film hasn't been released.
In the heat of battle, you really don't have time to decern who is man, woman or child, this wasn''t a law enforcement mission but, it was a military mission.
Boarding ships peacefully will usually be agreed upon before boarding by both parties, if this isn't the case then the ship in question will be considered hostile.
In regards to tear gas, this is up to the commander or operators on wether it should be used or not, there is no SOP in this regard because every scenerio will be different.
All said in done, the IDF botched this operation due to the fact they did not use over whelming force with the explicite intent of using lethal force at the first hint of resistants, if this was ordered then perhaps this would have never happened.