It's possible to alter your shortcut to automatically launch an application with the affinity you want.
The command I have in my target box of the shortcut is:
C:\Windows\System32\cmd.exe /C start "SWKOTOR" /D "C:\Users\Public\Games\SWKotoR" /high /affinity 1 "C:\Users\Public\Games\SWKotoR\swkotor.exe"
Obviously you'd replace the directory I have my swkotor.exe file in with the one yours is in in both places in the above line.
So it's a shortcut to the cmd.exe that launches what follows as a command. The command actually being executed is the start command, and the start command is what allows you to pick what CPU(s) to use for executing the game. The affinity integer is a bit flag, with the least significant bit representing the first CPU and going up from there.
You need to run this shortcut as administrator as well.
The actual game executables will run in compatability mode/as administrator since you should have set those properties already if you followed the steps outlined in the second post.
Since it's a shortcut to the cmd.exe, the icon will be for cmd.exe. To change it to the swkotor icon you just open the properties for the shortcut, click on the change icon button, and browse to your swkotor.exe and select the icon to change it.
Obviously this will work for any old game that doesn't work well on multiple cores.
Edit: Forgot to mention, this is for Vista. I'm not sure if anything has changed with the start command on windows 7.