I just followed these steps with XenApp 5 FR2 on Windows 2003 and it worked perfectly! Nice work!

@hfedrizzi - The MSI is not on your system (unless you copied it there). It's on the installation media. I just copied the file to the server and ran the commanded above. For example, copy it to the root of C: and then run:
msiexec /x C:MPS.msi CTX_MF_FORCE_SUBSYSTEM_UNINSTALL=YES