I do not know of any organic fungicides that can be used against botrytis. I have used Dithane which is based on Mancozeb to control fungal infections in plants. I would drench all plants thoroughly with your chosen fungicde some days before you lift them. Your coral pink pellie could be lifted and potted up and kept in a light, frost-free environment. Fungal infections in plants can usually be controlled but a cure is more difficult to achieve

With any sign of a problem, that part of the plant should be immediately removed to lessen the chance of ?? spreading.

The flower heads at the first sign of how you describe should be pinched back. The leaves also should be removed.

The plant, given full sun, and promoting new buds and leaves should be carefully watched for any sign of re-infection.

I've never heard of "botrytist" in geraniums. If you encounter any further sign of a problem, why not just speed up the winter care and remove the plants from the soil and wash off from the roots all soil there.
Then put them somewhere to dry thoroughly before storage.

A dusting of a fungicide could then be applied if you feel its necessary.
I understand in some parts of the U.S. "benomyl" has been removed from the market.

A garden sulfur I imagine would suffice.

I normally throw all my potted plants soil into the compost bin and use fresh when re-potting but since you think there's possibly something in the soil, I would suggest you throw this soil away....never to darken your door again.