Newton was no atheist. Newton's theory of gravity is about attributing that things are falling down due to God. Newton wanted to explore God's nature.

God fits into it as well as he did in Aristotelian physics in which educated people believed before Newton came along.

Newton did get into trouble for suggesting that the heavens follow the same laws as things on earth got he didn't go against the idea of God.

Newton himself was a theist who attributed things falling down to God. Although he claimed "hypotheses non fingo" ("I make no hypotheses", or possibly "I feign no hypotheses") for why gravity actually works, he seemed unafraid of implying that it was in some way a function of the Holy Spirit. Still, I'm unaware of anyone attaching moral significance to gravity, whether before Newton or after.

Well, except Yvain, but that implication runs the other way!