Why do you need to do this? To me, actually, subtraction needs justification, instead of trying to justify not subracting. If you want to see the effect without ground plane, you already have it. This way you take the direct ground plane reflection out, but leave the coupling terms in there. Ground plane is now a part of your structure now. In your reference paper, are the results given after subtraction?
If you are going to use the reflectarray with the ground plane, then you should be checking and designing in the presence of the ground plane.