I would like to remove Empathy from my Ubuntu system, (I am currently running Quantal without Unity, just Gnome). When I try remove it in Synaptic it also wants to remove Gnome-Core, which I assume will break my setup.
Am I correct?
No you are not correct.
gnome-core is in fact a meta-package, have a look at this url for adidtional information on the gnome-core package: http://packages.ubuntu.com/search?keywords=gnome-core
Info on meta-packages: https://help.ubuntu.com/community/MetaPackages
You can safely uninstall Empathy and the gnome-core meta package.
I believe gnome-core is a meta-package. It just makes sure certain things get installed. I don't believe removing it will remove anything else.