Sometimes, the MunkiStatus progress bar over the login window can get stuck, and pressing the Stop button can take a while to halt the progress bar completely.

To kill it immediately, press Cmd-Option-Shift-Escape (this is a slight modification of the usual force-quite key combination, which is Cmd-Option-Escape).

Full credit to Yehuda Bialik and Greg Neagle for this tip. The Wiki on Bootstrapping With Munki is now updated also to include a note this keyboard shortcut.