They only way to annihilate cheese would be, to make the game turn based all the time. Of course in reality it is, but outside of combat turns are so speed up, that you have free movement. This free movement is the core source for most of the cheese.
Other solution would be: If you enter a fight, you can transitioned into a 'battle arena' scene, which makes it impossible to prepare the fight heavily with tons of explosive barrels or whatever.
