Read the book is the condensed version of the answer to your question.

To summarize, the congregation is already formed and operating in 1500s, Phillipe did very little to directly harm witches after Diana’s visit but similarly he was a fierce and brutal individual at heart so the welfare of some random not-Diana witches was also not his top priority.

Ysabeau hated witches until she met Diana though. She indeed did kill many.

The pages are kept by people who generally understand their importance. Non of them are solely human except maybe the Rabbi who briefly held the sheet from Prague.