If anything, this should have been handled with the same Protocol when it comes to apprehending Criminals - Here's a US example.
Police are strictly supposed to attempt arrest and apprehension always, because a life is a life. Even Police officers are only supposed to use the appropriate amount of force, even if your suspect is fleeing... this isn't GTA where you can start firing off rounds just because someone flees - That's why you chase them. Police Forces only fire upon targets if the suspect is deemed an immediate and life threatening to themselves or to others.
Now Let's say that the they did feel threatened, PCG patrol boats are usually armed with a .30 caliber machine gun. Tell me what you think is appropriate defensive measures at the threat of being rammed (take into account that 10 rounds hit the port side of the vessel).
well I think that disabling the engine in an attempt to stop the ship, a fair decent attempt at self defense - But personally I think the 52 rounds that riddled the Port and Front of the Vessel in a wide bullet spread (as investigations currently show) is a tad bit excessive don't you think?
another point everyone forgets to ask, Did the PCG see any alternatives to shooting? Perhaps taking evasive maneuvers? the PCG Ilocos Norte-class patrol boat can move at 25 knots after all... much faster than Fishing trawlers usually...
I think it is too early to speculate what actually happened. It was not that the coast guard shot the vessel immediately. If you see from the investigation map, there were approximately 5 hour gap before the shooting (05.00 to 09.45), we don't know when was the chasing actually happened. Even after shooting, there were 3 hour gap before the incident being reported, a total of 8 hours since the intrusion. A lot of things could happen during this 8 hours.