You are missing the point. Newton didn't look for a miracle from God to explain what he couldn't. He left it up to later scientists to find a naturalistic explanation, and they did.
Newton believed that you could learn more about God through the study of His creation through the scientific method.
He believed God created the nature and it was up to us to discover it. That attitude has absolutely no conflict with the naturalist view that creationists hate. Whether it all happened naturally or God set everything in motion, it will all look the same to us, and we will come up with exactly the same results. This is because, as I said before, God is outside of the system we are investigating, just as the CEO of the lab is outside of that mouse's box.
Miracles happen, prayer gets answered.
That's great if the belief helps you. On the other hand, crazy and highly unlikely stuff happens, and it often gets interpreted as intervention. It's the old George Carlin skit, players always thank God when they win the game, but you never hear "Jesus made me fumble at the line of scrimmage." God put that pilot on the Hudson plane to save everybody, but nobody thinks he purposely put a crappy pilot on that other plane that crashed a couple weeks later.
Me, I hoped to finally have a boy, and I did. Had I been religious I would have seen this as a prayer being answered. I think I just got lucky. Or maybe the Invisible Pink Unicorn (PBUHH) touched me with Her horn and granted me a boy.
That gives you away.