You should be able to use thinreg.exe (a native ThinApp tool) to perform package registrations..
You can run thinreg.exe in a login script and to further enhance it can you implement the ThinApp SDK if you want.
Below will you find some more details:
http://blogs.vmware.com/thinapp/2008/10/thinapp-thinreg.html
http://blogs.vmware.com/thinapp/2010/04/simple-thinregexe-login-script.html
http://communities.vmware.com/community/vmtn/developer/forums/thinapp