It's actually quite easy to work out why the silver sword is used against the Aen Elle, in the past (1500 years before Geralt's time) we had the event known as the "Conjunction of the Spheres" a cataclysmic event which trapped many monsters and creatures from another dimension or "world", if you like, in the witcher world. Now we know that the Aen Elle are from another dimension, and travel to the witcher with the help of navigators. How they do this is like creating mini "Conjunction" like events so they can travel to the witcher world safely. Now because they are traveling in this fashion and also because they are from another dimension, much like many of the monsters and creatures that Geralt faces, the witcher world views them as outsiders like those same monsters and therefore that's why he uses the silver sword. They are not of his world so silver sword and elemental oil, quite logical and simple once you put the clues together.