If I remove transmission-gtk it shows a long list of packages. It want to remove gnome completely. Is there a meta package I can install to keep my system together and I can remove an application that is "part" of gnome?
The gnome package is a metapackage that depends on transmission-gtk. So by removing the transmission-gtk package you cause the gnome package to have broken dependencies so it is removed.
There are two ways you can solve this. You can either use the tools in the equivs package to create a dummy package to fulfill the dependency or you can mark all of the packages that the gnome package depends on as not being automatically installed and then remove the gnome package (by marking them as not being automatically installed they will not be removed when you remove the gnome package).