Toggle Natural scrolling from command line with reload
The same setting is visible in the Magic Mouse and Trackpad panes. This works if you have a Magic Mouse connected (but not if you do not):

osascript -e 'tell application "System Preferences"
    reveal anchor "mouseTab" of pane id "com.apple.preference.mouse"
end tell
tell application "System Events" to tell process "System Preferences"
    click checkbox 1 of window 1
end tell
quit application "System Preferences"'


This works if you have a trackpad:

osascript -e 'tell application "System Preferences"
  reveal anchor "trackpadTab" of pane id "com.apple.preference.trackpad"
end tell

tell application "System Events" to tell process "System Preferences"
    click radio button 2 of tab group 1 of window 1
    click checkbox 1 of tab group 1 of window 1
end tell

quit application "System Preferences"'


nb: the "Accessibility Inspector" tool that comes with Xcode can be used to locate UI items to click on.