Github's tagline is currently "Build software better, together." Wouldn't this help people create better software?
I'm not saying they should automatically add secret_token.rb to gitignore, just that they could let you know you might not want to do that.
I believe that a better idea is to fix this in Rails. Why is a secret key loaded from the configuration directory? I agree with ajross's comment (http://news.ycombinator.com/item?id=4970347).
This isn't to say that Github should do nothing to control the problem, but more must be done than just that.
Just not publicly viewable
If it's a public repo, don't check it in. I don't think Github should try to create a manifest of all "dangerous" files.
Really, best practice is to not check in sensitive values to your repository, ever, and instead use environment variables or symlinks to shared files via Capistrano to set these values in your application.
People so easily annoyed by trivial (yet potentially helpful) things should be annoyed as much as possible by the rest of us.
you can annoy some of the people all the time, or you can annoy all the people some of the time. You can't however annoy all the people all the time.