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You can uncheck enable SS in the pref pane and relaunch your apps. IMO however, it should relaunch finder/dock on uncheck if you have that preference checked... it is kind of unintuitive.
You can also delete the preferences for the app in your /Users/<user>/Library/Preferences folder. The just look for the shapeshifter prefs. Log out or restart and aqua will be back.
Side note:
I really am enjoying the 'safety' of SS's implementation.