I think it may be to protect the baby, because the threats of violence against Terri on the internet are horrific. If the baby was with her, and someone acted on a threat, it would put the baby in danger.
The other reason would be to avoid having a judge rule explicitly that she can not so much as see her child. This would allow her to go back, presumably after clearing herself in Kyron's disappearance, and request partial custody or visitation without that 'black mark' of a judge's explicit ruling.
It's not as if baby K is with a bad parent. Kaine is a good person, so she knows that baby K is being well taken care of right now.
If you love your child, you put aside yourself, and how much you want to see them, and think about and do what's best for them. Right now, considering the above, as well as the mess she's in the middle of, and no job, no home, etc, baby K is in the best place.
Terri may not be thinking of this as a long-term thing, but a short thing - just a few months.
Mostly, though, I think she's taking the advice of her well-reputed attorney. I'd take his advice too.