opposition to Yidden learning Torah solely because of who the initiator was brings into question the motives of his machlokes, whether it was a machlokes Lsheim Shomayim or not.
The Halacha is that when one is judging the actions of a Talmud Chochom one is obligated to judge his motives favorably. HaRav Shach was a Gadol by any standard we have. You are therefore obligated to judge his motives favorably. The fact that he was not infallible is besides the point. You are welcome to quote Gedolim who disagreed with his position but you do not get to question his integrity.