Since this has become a political issue with significant repercussion for PTI and IK, the best get out of jail card, ideally, would be for Atif Mian to declare himself that he is Qadiyani and his allegiance lies with Pakistan and he is the firm believer in the constitution of Pakistan and its deliberations (which by default declare him disbeliever). This will blunt all the opposition as he will be advising PTI government as a minority.
Otherwise, replace him promptly. There are many who can fill in the position. Whatever needs to be done, should be done quickly. As for PTI they needs to do their deliberations and background checks properly in future.