In order to get the mouse working correctly, you must go into the game folder and find the swkotor2.ini file.
For mac users, in finder, click "go" on the menubar and copy and paste this command in (without quotes):
"~/Library/Application Support/CrossOver/Bottles/Star Wars Knights of the Old Republic II The Sith Lords/Program Files/Steam/SteamApps/common/"
Once you are in the common folder find the swkotor2 folder, and find swkotor2.ini, open it with textedit, and change the setting: EnableHardwareMouse from 1 to 0. save the file, click exit, and enjoy :)
For linux users, it is exactly the same, except for the different locations where the bottles are. If you click manage bottles while in crossover, and then open c_drive, you can find the file the same way.