I always thought that the Blue Fairy gave Bae the bean because he was trying to get Bae to convince Rumpel to go to the Land Without Magic thereby getting rid of the Dark One.
Good point, I had forgotten about this. But as I said, it was her reluctance to hand over the bean that struck me. It could be because it was the last magic bean she knew of, though. Still, Emma was/is needed to defeat the Black Fairy.