I was researching this the other day myself. The game can be installed at the command prompt by using an -lgntforce tag. Unfortunately, the game still will most likely not run because of an incompatibility between Win 2000's CD-ROM drivers and the copy protection used in System Shock 2.
Looking Glass is releasing a patch for the game soon, though that will remedy this problem as well as fix a number of game bugs. Check out their FAQ for more info.