Fox News states that this ban came in place due to shop owners telling the government how the games are representing their country.
A translated article from a Middle East digital media has stated:
The Association has always boycotted these types of films and games. These (games) have been developed against the country’s national unity and sanctity. The games (“Medal of Honor: Warfighter” and “Call of Duty: Black Ops II”) have been developed against Pakistan, and the association has completely banned their sale. Shopkeepers are warned and will be responsible for the consequences if found purchasing or selling these games.
Call of Duty and Medal of Honor both have a few sequences in Pakistan. More importantly, the newest Activision’s latest title, Black Ops II, also has many sequences in Pakistan showing them as the hotbed of terrorist activity. Activision’s most popular title will no longer be sold in Pakistan, leaving Activision without one of their major market in the Middle East.