I've solved this by using user-specific folders, in the XDG fashion (
http://standards.freedesktop.org/basedir-spec/latest/ar01s03.html), using symlinks between shared game data (in /usr/share/games) and the XDG data folder of the current user (~/.local/share) and chdir-ing to this folder before starting the DF game. I've also started to add a "mod" mechanism to allow easy graphic mod managment (default, mayday, ironhand, etc.), but it's still in an experimental state.
I still had some issues with the SDL 32bit libraries that are not all available on amd64 arch, and I asked the maintainer of the ia32-libs package if it would be possible to add them, but without response so far. Have you solved this one, or are you packaging these libraries with DF ?