There's still hidden preference keys for changing the default fonts and font sizes.
defaults write com.apple.Safari com.apple.Safari.ContentPageGroupIdentifier.WebKit2StandardFontFamily Georgia
defaults write com.apple.Safari com.apple.Safari.ContentPageGroupIdentifier.WebKit2DefaultFontSize 16
defaults write com.apple.Safari com.apple.Safari.ContentPageGroupIdentifier.WebKit2FixedFontFamily Menlo
defaults write com.apple.Safari com.apple.Safari.ContentPageGroupIdentifier.WebKit2DefaultFixedFontSize 14
You could also set a CSS file like this as as the default style sheet in the advanced preferences.
body {
font: 16px Georgia;
}
pre, code, tt {
font: 14px Menlo;
}