Yep - the AQ GCS comes as a stand-alone exe.
However if you previously installed the original QGC you can remove it with the uninstall.exe and wipe the x86 program folder.
It leaves 2 entries in the registry though:
HKEY_CURRENT_USER\Software\QGROUNDCONTROL\QGROUNDCONTROL
and
HKEY_CURRENT_USER\Software\OPENMAV\QGROUNDCONTROL
You can wipe them manually or use a registry cleaner like CCleaner:
http://www.piriform.com/ccleaner