Open up nVidia Profile Inspector, go to the Indiana Jones and the Infernal Machine driver profile (create it if it's somehow not there, and add indy3d.exe to it), and for Antialiasing - Compatibility (DX9) enter 0x000000C1

After that, the usual steps (setting the AA Mode to Override and Setting to your desired MSAA value) will get the job done.

Further testing may be required to ensure there are no bugs forcing MSAA this way, but I haven't noticed any at first glimpse.