Both of Thrall's parents were turning green at the end of "Rise of the Horde," it was probably enough secondhand Fel exposure to ensure Thrall would be born green as well. Apparently genetic infusion from a Mag'har specimen can undo the coloration mutation in some cases, although I guess it also depends on the length and severity of the secondhand Fel exposure (e.g. it might not work for Orcs who actively drank Mannoroth's blood the first time).