Yes, I do think that baby Charlotte/Angela has been literally showing failure to thrive because she hasn't been touched or loved enough by Mrs. Putnam (who hasn't shown any signs of maternal attachment, just frustration with and distaste for the child). It's a genuine and tragic pediatric diagnosis - anybody else remember Harlow's monkeys and their wire vs. cloth-covered 'mothers'? https://harlows-monkey.com/home/why-harlows-monkey/
I'm not surprised that the baby responded to Jeanine/Ofwarren, but the transition from NICU to happy healthy baby overnight seemed a bit too magical. I guess it was all those pious prayers pouring out of Gilead.