The problem for the control structures is they won't flow only what they were designed for. They will flow what they will flow based upon the head (elevation difference) between the two rivers along with other factors. Now if the structures are designed to move 620,000 cfs of water, but the head and flow rate of the rivers forces more than that through the structure there is nothing to stop the water. If this happens they are exceeding the design rating of the structure and it could be damaged. I think this actually happened during the 73 flood. Even though the river was no where near the Project Flood flow rate in 73, the increased head between the two rivers (due to the natural deeping of the Atchafalya channel and rise of the Mississippi) caused the flow through the low sill to exceed the capabilites of the structure. Morganza was opened to relieve this pressure (reduce the head) and the structure survived....barely. It was badly undermined, lost one of the inlet retaining walls, etc. This is why the aux. structure was built.
I'm not saying this IS happening, I'm asking how close we are. There are two issues here one is flooding Baton Rouge, New Orleans, etc., the other is stopping the river from changing course into the Atchafalaya. Honestly the second scares me far more than the first, as it would change life as we know it in Louisiana, and would be a terrible blow to the economy of the country at a time we can ill afford it.