It's really quite safe. In last three or four years, I have traveled almost all parts of Gilgit-Baltistan with my family and have never faced any problem. Gilgit-Baltistan is more safer than any other part of Pakistan. Rather I should say that it is the safest place in Pakistan. We can't judge the law and order situation of Gilgit-Baltistan by a very few violent incidents of Chilas. While travelling on the KKH, I had always preferred Chilas for a night stay and it was all safe.
Last month, I traveled from Lahore to Gilgit with my wife and three kids in my alto car thrice. It was safe. The only problem was a 50-km portion of KKH starting from Dassu. There the road was in a very bad shape. At most of the places, there was no road but potholes. The rest of the KKH was good.