There are few in Islamabad.
One of them is Metafitnosis (:::Metafitnosis:::), in F-8. They offer martial arts, There is one in F-11, I don't remember it's name.
Although I don't like owner of Metafitnosis, he is a real jerk, but the club has good facilities to offer.
Beside this, there are certain free style (without proper club) martial art instructors and few of them are really good. In case you want to know about any one, let me know and I'll post their numbers as well.