Science is inherently atheistic

[Deesse23]

Absence of evidence is not evidence of absence, without the tools and perspective to qualitatively evaluate.

It basically is, when there is evidence to be expected. The people who bring forward supernatural events argue that something supernatural has happened in our natural world. They are pointing to natural effects (of the supernatural), aka. the supernatural being in interaction with the natural world. With the scientific method we should have at least been able to confirm that effects have happened for which we had no natural explanation. I dont know of any event so far that couldnt have been explained by natural events (in absence of any evidece), and thus i feel compelled to stay with the most simple explanation with the least assumptions: So far nothing supernatural has happened, ever.

There have been things that were supernatural that aren't now. Does that mean that supernatural things don't exist? No.

These things never were supernatural in the first place, we just were ignorant of their naturalness. What i think about something has no infuence on that very thing. If my opinion on a thing changes, that doesnt change the thing per se.
Ergo, the fact that we were (and are) ignorant of things is not a good argument for the supernatural imho. Its a weak argument borderlining the argument from ignorance fallacy.

I believe the scientific method is great for testing the known natural physical world. It's great at falsifying superstition and bringing more understanding into our world.

Agreed. But its not only limited to this. Once we have falsifiable claims about the supernatural and once we have the tools to falsify, we can investigate the supernatural. Of course all-powerful beings, being consistent with anything (and thus any experiment, data or observation being possible evidence) will always stay outside the grasp of the scientific method, because they are unfalsifiable, and i am not going to change my standards for evaluating claims (about such beings) just because.

At one point sickness was supernatural. It was demons and angels.

It.never.was.

Then science corrected that to be smelly things caused disease, thus making it a natural explanations for the supernatural

No, it was looking for explanations for the unknown. You are stuck with the idea of "We dont know therefore.....", and that is fallacious thinking. It is never justified.

Supernatural can be a catch all for things we don't understand at the time, but that doesn't mean they can't be known

Q.E.D. with regard to my last comment above.
"We dont know" is the correct catch for everything we dont know. Calling it "supernatural" is sloppy thinking. Of course unknowns can be possibly known in the future, but calling them "supernatural" doesnt mean these unknowns will be revealed as "superatural" (as previously, ignorantly applied). Its sticking to sloppy thinking, shoehorning in what you want to be true into what may be true.