The Jews who wrote Genesis aren't the Jews who wrote the Midrash. The culture from which the myths concerning the Nephilim and Benei Elokim arose had no problem

The Jews who wrote Genesis aren't the Jews who wrote the Midrash. The culture from which the myths concerning the Nephilim and Benei Elokim arose had no problems with God having sons, e.g. Mot, Yam. The Jews of Elephantine are documented as having a temple to Anat, daughter of El (God) by his wife Asherah, in the 5th century BCE. The opposition to reading any of the Hebrew scriptures as referring to "Sons of god" likely arose as a reaction in Rabbinic Judaism to Christianity, both of which (along with Karaite Judaism) arose out of Second Temple Judaism.