I'm confused why you think anything will break. There would obviously be symlinks, so anything that's currently in /bin will continue to work if invoked with an absolute /bin path.
I consider linking across file system a very bad practice because if /usr gets errors all the symlinks may be broken until it is repaired. Currently / is 600 MB on my system /usr being over 12 GB nad merging will just make it bigger. So there are more chances to break /usr and it takes more time to repair it.
Aditionaly remount ro on error is hardly set in fstab and fs_passno is usually 2 not 1...
With what you propose, any /usr fs bug will end up inserting a CD or USB key for repair... For sure it is not the case at the moment!
Just as another reality check: I believe Red Hat has already done this. Lots of people use Red Hat and derivatives, and there doesn't seem to have been that much breakage.
Red hat is mainly for servers nowadays with paying support. So I wonder if you are really doing meaningful comparison. Likewise Systemd was used by various distrib before debian, and it did break a lot at the beginning when upgrading existing debian installs, most init script are still unconverted and they cannot really accommodate the /etc/defaut/pkg configurable options...
-- eric