SUMMARY
Add an option to kactivitymanager closing all activities except for the Default activity and expose it in the KDE settings.
That could perhaps also be achieved with a separate application using dbus (but not sure if that would happen early enough during KDE startup) or a hack which edits the configuration in kactivitymanagerdrc .

MORE INFORMATION
I am using KDE activities extensively. There is essentially one for each project I am working on. The most significant issue I am having with it is that it will behave really badly when KDE crashes or I restart KDE without remembering the open activities. This is because after the crash kactivitymanager will attempt to open all previously opened activities with all the associated applications. This can fail badly if for instance at login the resources from which files where loaded are not available yet (e.g. external media, crypto containers). In this case you get a lot of error messages which is very annoying and implies that you loose the open windows. My workaround is to edit ~/.config/kactivitymanagerdrc on a shell before logging into KDE, but that is quite tedious as well and I tend to forget it.