OS X 10.9: Deleting Keyboard Input Sources
If others got here searching for how to disable all input sources except a custom keyboard layout, you can edit the com.apple.HIToolbox plist:


Change the current input source to your custom keyboard layout.
Open ~/Library/Preferences/com.apple.HIToolbox.plist (in 10.9) or ~/Library/Preferences/ByHost/com.apple.HIToolbox.*.plist (in 10.8 and earlier). You can convert the plist to XML with plutil -convert xml1.
Remove the input source or input sources you want to disable from the AppleEnabledInputSources dictionary. If there is an AppleDefaultAsciiInputSource key, remove it.
Restart.