I wasn’t aware of problems with kpackagekit, other than it sometimes claims to be unable to connect to dbus. Thank you for the information so that I can avoid using it in future.
I am using KDE4, but I also need to use some applications that depend upon KDE3. Similarly, some applications need Gnome and I have some that expect Motif.
I suspect you are right about the path you suggest. It would be nice just to be able to revert a change and know that one was back to the original state.