The source to the game executable (rendering, script interpreter, physics, pathfinding) is free and released under GPL. The assets, however, such as scripts, textures, shaders are still under the original commercial license.
It is certainly possible to make your own media for the game; it will be a lot of work, but arguably less work than writing your own game engine AND making the assets. It makes sense because the Doom3 engine is very flexible and you can do a lot with it, some of which has already been done in the form of mods (as the SDK has been available for a long time).