Anyway , if the way you play sounds normal (no harmonics or wierd noises at the background) , then it's ok.
I hold my pick normaly between index and thumb , leaving about 1/4 of the pick (in terms of length , not volume) exposed , and when I do Pinch Harmonics , I just roll my thumb a little closer and angle the pick so that its pointed edge is slightly looking down.
I never faced the problem of unintentional thumb rubbing the string before , but I think you just need to let a little bit more of the pick exposed ... i.e. You probably hold your pick with your thumb too close to the pointed edge.
Be carefull not to have your thumb too far , so you don't get problems with your P.H. technique.
