It is a bad decision to ask him to step down, but a worse decision to have hired him in the first place. Not because he is a Qadiyani. But because the government should have known that they would not be able to withstand pressure from those who were going to exploit the situation against the government. They had already seen what happened the last time IK mentioned Atif Mian. They should have anticipated this.
There would have been absolutely no controversy whatsoever if they hadn't hired him in the first place. But now they are seen as having buckled under pressure from the opposition, thus showing their own weakness and emboldening the opposition. They have disappointed a large section of their support base (the more "liberal"), and alienated the minority communities (not just the Qadiyanis). All in all, this was a mistake.
Atif Mian's qualifications and expertise in this whole affair has become almost irrelevant.