Yeah, no.

Newton was such a complex human. He seemed capable of holding many, sometimes opposing beliefs, at the same time.

Newton's conception of the physical world provided a model of the natural world that would reinforce stability and harmony in the civic world. Newton saw a monotheistic God as the masterful creator whose existence could not be denied in the face of the grandeur of all creation.

There's even a Wikipedia page dedicated to his religious beliefs.

https://en.m.wikipedia.org/wiki/Religious_views_of_Isaac_Newton

If you are into learning about him there's also a rather good read, The Janus Faces of Genius, by Betty Jo Teeter Dobbs, that looks into his occult work.

Furthermore, for the sake of complexity, we can look into how, when he was the warden of the mint, he became responsible for the deaths of 19 people. He turned a largely ceremonial role into a task force, chasing down forgers and sentencing them to death.

discovering how physics works doesn't necessarily dis-prove the existence of a supreme being that designed the laws of physics

I've said many times in my life that I hate all religion...But Jesus lives under one of the couches in my house so I guess he might be real.

I asked him what he was doing down there and he told me "I'm hiding from the Christians"

He likes to watch me play video games, but he can't drive himself to actually play any of them. He doesn't like violence...not even computer-simulated violence.

"So then gravity may put the planets into motion, but without the Divine Power it could never put them into such a circulating motion, as they have about the sun"

Nah, he rationalized the shit out of it

How was it refuted?

God cannot be refuted nor confirmed. It's like unicorns, elves, dragons, and many other myths: we have not seen proof of their existence, nor have any claimed proofs of their existence been confirmed to be a valid, but that doesn't rule out that we will never find proof.

Such is my understanding science: there is no absolute certainty nor absolute confidence. I think only logical fallacies might never exist e.g an all-powerful creator immediately runs into the logical problem of "can god create a rock that it itself cannot lift?".

But what if our universe were just a simulation within a machine of a highly advanced species? Their ability to modify the simulation to their will might make them akin to gods for us, but that also incurs the question: what if they were in a simulation themselves? That can be repeated to the root until a "real world" is reached, but that still leaves the question: how did everything come to be?
We can thus cut out all the "if god exists, who created god" and focus on a world without the need to get distracted by the god problem.

Mental compartmentalization is very annoying.

This is the bullshit that fundies are accidentally pointing to when they claim all the great scientists were theists