i'm sure there are complications for childbirth at such a young age.
There definitely are.
Just because the mother is young and small doesn't mean the baby won't grow to a normal size (or attempt to, being limited by the mothers size).
The article states that the girl is 4'6", and the average length of a healthy baby is 19-20", or 1'7/8".
In comparison the average US pregnancy is at age 25, and average female height is around 5'4".
since when is the child of a raped stepdaughter in the hands of the government
shouldn't this really be in the hands of the mother or the girl
The mother was arrested, for enabling the abuse.
The girl therefore has no legal guardian, so she is under the care of the state.
She's a legal minor, therefore she requires a guardian.