How to disable Mission Control shortcut

Did you try double-clicking on the actual keyboard short cut for that function in System Preferences/Keyboard/Keyboard Shortcuts? You can change the key combo at will. Of course there is no guarantee they will take, just as your "Restore Defaults" did not take.

I use Spark, a free app that lets me map anything I want, and overrides the OS settings. If there is a con flit (which shows as the yellow triangle/traffic cone), I change the OS conflict to some unused combo.

I complained to Apple that I could not change those keyboard shortcuts to "Open app X". The response was that I should not try to do that, as the existing system was working as designed.

This is not a built-in cure using the native OS options, but it works.

If you use Better Touch Tool, you can configure a shortcut for the keyboard, mouse, magic mouse, trackpad or even Apple remote to close a window, and it will work in Exposé.

BTT is free and it works really well, in my case I configured the close shortcut as a pinch out gesture for my trackpad.