There are plenty of situations where averaging two safe-but-opposite inputs would cause a crash. For instance, if you're holding hands/handcuffed with someone and walking toward a pole, you must both either go left, or both go right. This is a very common scenario in life and we have many solutions for the problem.

In the Air France situation, there's no way for the plane to "know" which pilot's input is correct, so I don't have a good answer, but "just average two drastically different inputs" seems crazy.