There is a fine line between attempting to have Assad be removed and destroying the armed forces and the organs of state. Look what happened when they disbanded the armed forces and started debaathification in Iraq. And remember the USA, UK, France etc are fighting ISIS in the north and oppose many of the other Jihadist groups - who would move into the areas currently held by the state if they were rendered defenceless?
Punishing them for using CW against the CWC is not the same as destroying them.