Yes, it is "unfortunate" that telling the smart, highly trained , most educated and strongest military ever, who have weapons so 'smart' they hit exactly where they are aimed is not enough. Yes, telling them  exactly where you are [ MSF: We are STILL in the big hospital standing alone with the big red cross on it just like for the last couple years.] Then, after the attack started the doctors begged them to stop but that was not enough to keep the group of doctors and nurses and patients from becoming collateral damage. 

Your first paragraph implies that there were, at least likely, armed militants taking military action from the hospital.  The last I heard the spokesman for MSF said they were unaware of any armed soldiers in the hospital and did not know of any fire from it. The fog of information is deliberately made thicker than the fog of war but far more so by politicians and Generals than by doctors. There are video and audible tapes that would reveal the truth [remember Bradley Manning?] if enough people wanted the truth badly enough. If there were muzzle flashes coming from the building it could be proven though it would still not establish a justifiable reason for the attack on that hospital. If the videos proved there was reason for the attack we would have seen them by now.