Safari stores favicons in a database named ‘WebpageIcons.db’ located in the folder: ~/Library/Safari/Icons. It is possible to disable the creation of this database with the following command:
defaults write com.apple.Safari WebIconDatabaseEnabled -bool false
Delete the current database after applying the command:rm ~/Library/Safari/WebpageIcons.db
Relaunch Safari application for changes to take effect.
Restore the creation of favicon database with:defaults write com.apple.Safari WebIconDatabaseEnabled -bool true