What's the reason for tying some applications to GNOME?
Both the gnome and gnome-core packages are meta-packages. Removing them does not actually remove any installed programs.
Briefly, meta-packages are a way of bundling multiple packages together. Installing a meta package will install these other packages but removing it will not actually uninstall anything. Synaptic is selecting them for deinstallation because one of their components is being removed. However, you will find that no other packages are removed and you will still be able to use your Gnome desktop.