I think that's an oversimplification. There are definitely cases where some thing started as a daemon under a user session, graphical or not, should be killed to be safe. For example, ssh-agent.

There are other things that are meant to be left around, as that's their purpose, such as screen and tmux.

I would say the safe solution would be to kill everything in the user session at multiple levels (GNOME, and user session management demon like logind, etc), and to provide a defined safe way for the very few programs that want to stick around to do so. That seems like what systemd came up with as well.