Even the best photographers take bad pictures from time to time. If you know for a fact that you want to delete picture 111 from CF1, then it should be deleted from CF2 as well. Otherwise you end up with files that you do not need or want. Those files take up space on your back up HDs and while one or two may not make a difference, they will soon begin to add up. Plus, it is a question of time. If you know for a fact that picture 111 is a throw then, it saves you time to make that decision just once, and on the camera.
At the end of the day it is a flasghip camera so it should be customisable, so I do agree that when they do implement this "fix" they allow users to choose how the delete works.
Oh, I delete plenty of images.

My point is that for my workflow, not deleting the image from CF2 at the same time has no negative impact (because I don't transfer images from that card normally, it's only in case CF1 fails), and
might have a positive impact if I accidentally delete an image I shouldn't have deleted, it's still there on CF2.
But I absolutely agree that it should be customizable - that way, everyone gets what they want. I am just expressing a hope that Canon doesn't apply an irreversible fix for a problem I don't currently have, and thereby
create a potential problem for me.