She was a morale booster to be sure, but by no means the strategic leader of the army. There was a similar question here recently, to which I answered:

Joan of Arc was a tremendous asset to French morale, but she was by no means the principle strategist of the French war effort. The infamous Gilles de Rais (baron, favorite of the Duke of Brittany, Marshall of the Crown and serial child killer), one of Joan's companions, was in many respects a more conventional war leader whose influence on the strategic dimensions of the conflict is often overlooked in favor of the more poetic image of Joan as an inspiring commander.

In effect, Joan was a symbol, and that one the Crown was eager to subdue after winning the war. Her resurgence in popular culture is a considerably more modern phenomenon, and her induction into French national mythology distorted her role and caricatured her influence.