Going with an operator has both its pros and cons. On the pro side, everything is pre arranged. You dont have to worry about anything. The guide is with you to tell you about all the beautiful places. And they negotiate with locals for services which are not part of package like porters etc so you get discounted rate on that too. The one we went with was pretty reasonable. Stay was at Shangrila in chillas, Fairy Meadow cottages in Fairy Meadows and Eagle's nest in Hunza. All of these were good places with nice and clean environment. We got breakfast and dinner on time and was always good (Although it was chicken karhai everyday for dinner and we got kinda bored). They know all the routes well and being experienced drivers, the speed is usually faster. Another good thing is that apki gari bach jati hai. The size of potholes i saw on KKH, i am glad i didnt put my car through that.
On the con side, you cannot stop at every place you like for pics etc. The biggest problem might be about other people in the tour who are travelling with you. Luckily, we were a small group of 12 people including 3 couples. So it was a decent group and we got along very well. But in season, the groups become as big as 100 people so that might be an issue.
I will PM you details of some tour operators. You can check their plans etc on face book as well.