Unfortunately, decay is irreversible. It can not, and will not, heal on it's own.
The cells that made your teeth (ameloblasts and odontoblasts) died after they formed your tooth. They are no longer around to "do repairs" when your teeth are damaged. This is the opposite of other tissues, like bone, which retain the cells that formed them and can repair itself. The teeth in your mouth are subject to the simple chemistry of demineralization and demineralization. This can be done on a small scale, but not to fix decay.
The closest thing to an "all natural" treatment is
fluoride. Fluoride occurs naturally in the water (although some places add additional) and has been shown to significantly lower rates of decay.
Please keep in mind the that "drilling" a
dentist does in merely removing decay, which is your stated goal. A filling, literally just fills in the space that decay left. Just like everything in life, a filing will only last so long. The problem is not the filling itself, but new decay.
Best of luck. I hope you seek
dental care from a professional.