She can't join pregnant. If she still wants to join after she has the baby, she has to sign her parental rights over to someone while she's in basic and AIT. After that, everything depends on her assignment. If she's in a place where she can get her child back, then she can get her child back. If not, she'll have to wait some more.
Or you two can just get married and she can get the proper maternity care. Then your baby will be taken care of from day one without all the paperwork and drama.