I had similar issues (and more) with this quest as well. Although, it did remind me of a (real) fungus that I read about that seems to have metabolic processes feuled by gamma rays. Unfotunately I do not have the link, but I will edit in if I find it.
Now, to the subject at hand. As many have said, the BoS do not hate them, but rather they are, with a dash of distrusful disdain, indifferent towards non-ferals. The ghouls do represent the dangers of destructive technologies unleashed, along with the corruption of the legacy of makind through mutation. The preservation of this legacy is one of their most important beliefs. It is part of the reason that they gather tech, and why they value genetic purity. Their penchant for purity is borne of this, not Nietzschean pseudoscience. The BoS respose to ghouls is rater pragmatic, as they pose a security threat. They could, after all, could turn feral. The BoS does not always shoot them on sight, in fact they often tolerate their presence, so long as they do not offer any provocation. In short, they don't slaughter the ghouls, but they won't be winning any civil liberties awards.