It think it may be possible to do, though it would require a lot of fiddly work. It would require getting a copy of RivaTuner, and adding your desired program to the launcher. Then, you'd have to make a patch script with the desired settings i.e. your choice of AA, and link to that within the programs entry, and run the game from the launcher. I guess it would work, though I haven't actually played around with patch scripts yet, so I don't know what options will be available.

Either that, or use RivaTuner to change your level of AA before you enter your desired program. QED.