Get rid of them with
NPCReplacements=(FromClassName="Leedsichthys_Character_BP_C",ToClassName="")

you can also put another dinos class name in between the two " at the end to spawn something else in their place.

I myself usually just turn off their damage so they are still annoying but don't destroy rafts.
DinoClassDamageMultipliers=(ClassName="Leedsichthys_Character_BP_C",Multiplier=0.00001)
DinoClassDamageMultipliers=(ClassName="Alpha_Leedsichthys_Character_BP_C",Multiplier=0.00001)