Shimr, the son of Sahabi Zil Jawshan, himself is a medium in those hadiths.
And we have no issues with the notion that a believing person could father a non-believer or vice versa. A good example is Yazid's own son, Muawiya Ibn Yazid, who was a true believer and refused to sit on the masnad e Khilafat on the grounds that it only belongs to the Aal e Mohammad (saww).
He is not.