Ahsan Iqbal sustained a bullet wound to his right shoulder when was attending a corner meeting in Narowal's Kanjrur Tehsil.
Another suspect has been taken into custody for shooting at Pakistan's Interior Minister Ahsan Iqbal.
The Bethel Memorial Church has been the target of a terrorist attack in the past.
Pakistan called in the Army to restore order after violent clashes.
About 2,000 activists of Tehreek-i-Khatm-i-Nabuwwat, Tehreek-i-Labaik Ya Rasool Allah and the Sunni Tehreek Pakistan for more than two weeks have been blocking the Islamabad Expressway and Murree Road that connect Islamabad with its only airport and the garrison city of Rawalpindi.
Pakistan's law minister Zahid Hamid on Monday quit as the government "surrendered" to hardline religious groups, who called off their violent protests in Islamabad that had left six people dead and hundreds injured.
Pakistan Prime Minister Shahid Khaqan Abbasi assured the Secretary of State that his country is committed to the war against terrorism.