What causes chicken fat on the surface of soup, and does it add flavor to the dish?
Although the fat may add some flavor to the soup it also changes the mouthfeel. Instead of having a nice clear broth soup which is light and refreshing the fat in the soup with coat your mouth leaving a greasy feeling and taste. I cant be completely sure but if you were using the chicken thigh to just add flavor and not leave the meat in the soup you could use a chicken stock that your either make or buy from the store. As was stated above you could remove the fat from the soup. I would like to add another method to what Foodrules stated. 

-Take a metal ladle and fill it with ice. Dip the ladle into your soup being care not to go deep enough to actually get any liquid in the ladle. They key here is that the cold ladle will solidify the fat and have it stick to it. You just remove the ladle wipe it clean with a paper towel and repeat until the fat layer is gone from your soup. Its very effective and easy.