I also don't really buy the arguments for ENV storage of even non-sensitive data. There's just not really any good reason to do so; your config has to be put in place by some tool, even if it is in ENV; why not make your tool produce a file, with reasonable permissions in a well-defined default location? The 12 Factor App article seems to believe that config files live in your source tree, and are thus easily accidentally checked into revision control. That's not where my config files live. My config files live in /etc; or, if I want it to isolate a service to a user, I make a /home/user/etc directory.
One could say, "Don't store passwords in the revision control system alongside your source." And that would be reasonable. But, there's no reason to throw the baby out with the bath water.