Yes though the politics overshadowed it. Core issue has always been religious otherwise why the wish to join Pakistan?
I would though qualify it with independence being the intermediate step which they considered would be more palatable to india
Muslims were clearly divided on the issue of accession back then. Prevailing sentiment in the valley was to decide at their own. The tribal raid then came as a god gift to India. And today the wish to join Pakistan is less to do with religion but the grass is always greener on the other side.
So what do you prescribe?The problem of Kashmir is not Kashmir, but the existence of the Indian nation state created as a second hand British imperialism. Solve the root cause of the problem will resolve the Kashmir conflict. Fight the disease, not the symptom.