User blog comment:RunicVamp/Is Billie really Death???/@comment-1975828-20160813085845

In "We Happy Few", Amara took down the Bunker's defenses so she could enter. Sam and Dean didn't appear to be aware of this and left the Bunker unprotected.

As for Billie, she seems to work on her own, being her own agent. She sided with the King of Hell because of "tough times". It kind of shows she is not a leader of someone, but simply trying to survive. Unless we see another reaper, we can't confirm that, but I doubt she's Death.

As for why Billie is important, check out Rowena, who has had more screen time than anyone besides Sam, Dean, Castiel and Bobby Singer. They kept Billie because she was useful to the plot, likely.