Actually, I think the fairies are a bunch of screw-ups that act like a bunch of demi-gods. They do it “for the greater good” but the road to hell is paved with good intentions. Several of the magic users, if not all of them have stated at one point or another that “No good comes from magic”, and they have the scars to prove it. Yet the blue fairy refuses to acknowledge that, and stubbornly persist on using it. Every time the fairies make a mistake, evil is created. It’s how the dark one came to exist, that girl Bae talks to names her as the source. Once evil is brought in the world, the fairies can’t undo it, except send you to another world.
Another example: Look at poor Dreamy/ Grumpy. He got messed up by a hit of fairy dust, and now is forever miserable.
So I don’t think that the fairies are bad, just extremely meddling busy-bodies, that can’t oversee their actions. And that leads to casualties. And who knows, maybe they are just fairy-dust addicts, even more addicted to magic than Rumpel.
The do look a bit drugged up in those suger-coated jellyfish outfits, don’t they? 😆
BTW if I remember correctly the Blue Fairy states only that it is “The last known bean”… there might be dozens of them laying in ditches throughout FTL