I'm not sure what you mean by default GP.
I suppose the trick would be to consider the various folders that can be redirected and then only redirect those for which you see value in your particular environment. It could be that you choose not to redirect desktop folders in the future. However there is more likely value in leaving desktop redirected. Whilst they are redirected, if connectivity to the server is lost (server reboot, IP phone with built in network switch glitches - whatever... -the desktop will glitch in the way that you describe.
Personally, I'd live with it (and if the users complain, boom "WHAT!!??? YOU DIDN'T LOG OUT WHEN I TOLD YOU I WAS GOING TO DO THE SERVER UPDATES!!!" )
When using redirected folders on portable computers, it works best if you enforce off-line folder caching - but I'd not do that for desktops - too many issues with systems staying off-line and users complaining about files missing etc..)