Just upgraded from Yosemite to El Capitan, and I started out with an Emacs problem: it wouldn't launch from the Emacs.app icon, complaining that it couldn't find /bin/false. I tracked this down to the fact Emacs.app was trying to run /usr/bin/login, the default for the "Terminal" app. I can switch "Terminal" to run /bin/bash, but that doesn't solve the Emacs.app problem or similar problems for any other apps that try to run /usr/bin/login.
It looks like I need to fix /usr/bin/login to run /usr/bin/false and not /bin/false, but I have no idea how.
I tried to trick the programs backwards,
sudo ln -s /usr/bin/false /bin/false
and I get "Operation not permitted." I tried
sudo cp /usr/bin/false /bin/false
and I get "Operation mot permitted."
I'm stuck looking for "the right answer" or for other work arounds.