You have to understand the change in circumstances. Qadyanis hadn't openly declared rest of the Pakistani muslims Kafirs during Jinnah's time.
It started when Qadyanis attacked a train back in 70's.
Qadyani 'Khalifah', on the Parliament Floor, in 1973, declared that all those who do not believe Mirza Ghulam to be a nabi are kafir. This resulted in even a liberal Bhutto to fully support the clauses in the Constitution declaring Qadyanis non-muslims.
Ever since then, Qadyanis have been spewing venom against Pakistan.
Qadyanis do not consider themselves to be a minority, and lay claim to Pakistan as a majority. Their belief is that all non-qadyanis muslims are kafir. This is no small issue!
Due to this, the majority has grown intolerant of Qadyanis and restrictions have been placed on them to keep peace. Jinnah went against Congressi Mullah, and he would have gone against Qadyanis as well had he been alive after what they been doing since independence and especially after new constitution was written.
Having a different belief system is one thing (once a new nabi is introduced, it is no longer Islam) but masking it as Islam is deception, fraud and identity theft.