So what is wrong in it, mention one wrong of it.
How it will be counter productive for India ?
Several ways
In Pakistan
1. Minorities in Pakistan will not be allowed to visit India on religious grounds. This is the way many refugees escape Pakistan
2. Minorities in Pakistan will be persecuted, like many mandirs and hindus were killed in Post-Babri violence
3. Minorities religious institutions will be shut off to Indian pilgrims.
In India
1. Patriotism will be proved by being as hostile as possible to Pakistanis. Those who aren't will be called traitors.
2. Any religious institution which allows Pakistanis will be seen as traitors.
3. Radicalization of the society. Extremists will be dictating agenda, and liberal attitudes and sensibilities will be wiped out
4. Religious institutions and their functioning will come under dictate of extremists.
5. Places of religious worship such as the Ajmer Dargah, are open to all, and the rights of admission are solely dictated by the Govt.
However, if Religious institutions do want to be political, they can start by declaring politicians as heretics, and bar their entry. It is in fact the politicians who have caused us most harm.