Because you can't have 28,773,245 options for everything. Not everything will end up being moddable either. Some parts are simply core gameplay elements which are not suited for toggling. Friendly Fire is an critical part of the entire combat system. It is crucial for game balance, which means it is not possible to just turn it off and keep everything else the same.
I don't think FF is that critical. I know several games, where you can simply turn in on/off via options
