Gnome-shell is a dependency (suggested) of GDM3. Mint switched from GDM3 to MDM as the default DM a while ago. MDM does not have all those Gnome dependencies.
I'm also using LMDE XFCE and made the switch manually awhile ago and am not having any Gnome dependency issues. To make the switch do the following:
Install MDM. If you do this via Synaptic then you should get a pop-up asking which one you want as default, GDM3 or MDM. Choose MDM.Reboot
You should then get the MDM login screen.
If all went well you can then uninstall GDM3. Then try the upgrade again.
Hope this helps.