I see you have comments on both answers asking about applying changes to all CKEditor instances. The following code should allow you to override settings for all instances
window.onload = function(){
CKEDITOR.on('instanceReady', function (ev) {
ev.editor.setKeystroke(CKEDITOR.ALT + 48 /*0*/, false);
});
}
Every time a CKEDITOR instance is initialized and ready, it will automatically disable alt+0.
There is a list of the ascii codes for the different characters here for reference if you want to disable other keys: http://en.wikipedia.org/wiki/ASCII#ASCII_printable_characters
Use the number in the Dec (decimal) column to disable they key in the Glyph column.