You say it also requires steam to run, if so, add it to steam library, then try installing it through steam. (Click on the Games menu at the top, click on Activate a Product on Steam, and put in the game key). This could bypass the problem if you are currently installing from disc.
Otherwise, as BFG10K said, if you already have a current version of DX9, the install from disc should not try and overwrite it, so don't know how to get around that.