The source code for the engine should compile without the assets. Or at least with some minor modification to the source tree. Take a look at these other commercial games who have released the source code of the engine but kept the assets proprietary:
https://en.wikipedia.org/wiki/Duke_Nukem_3D
https://en.wikipedia.org/wiki/Doom_%28series%29 (1, 2, and 3)
https://en.wikipedia.org/wiki/Quake_%28series%29 (1, 2, 3, and 4)
I'm confident that there are others but I can't think of any off-hand. These open source contributions are a gift that allows the open source community to create ports to initially unsupported platforms and to enhance the engine. Have you checked out any of the enhanced doom ports? (http://dengine.net/). There are even user-contributed HD assets for Duke Nukem 3d (http://hrp.duke4.net/download.php).