You will find more info about the situation inside Pakistan on travel websites than over here. I don't know of any middle eastern airline that gives their crews night stops in Pakistan. Firstly it's close enough to fly turnarounds, and secondly the security situation in the country is quite bad, especially in Karachi, I hear the Lahore and Islamabad are better. And forget about the North West Provinces, the government barely has control of that region, and in some parts no control at all.
As for diseases I would stick to bottled water, most of the diseases are spread though water. If you are eating out avoid foods that have a lot of water e.g. soups, currys etc. and don't let the fancy name on the outside of the hotels fool you, they get their water from the same source as the local kebab hut down the road, it's just the price and decor that differs. Malaria is the other big one. The disease situations is similar to Africa. Get shots if your overly worried.
Keep a watch out on embassy websites for travel alerts, and keep updated with the political situation. It would also be a good idea to avoid crowded places