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.
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.
GitHub will already generate a .gitignore file when you create a repository on its website. It would be nice if the .gitignore file was based on the type of project being created. And it would be nice if it gave a warning when files that are in the default .gitignore were being pushed to the repo.
If the filename changes in the future, who cares? It defaults to the current situation where no warning is given, but potentially improves security in many cases. And it's not a big deal to add another file to a list.
Right, but how does it know that? There is no "Create Ruby on Rails project" command in git. How will it know what to include? Will it have to scan and somehow detect that it's an RoR project? And check the version of it?
Much simpler to leave this stuff to a RoR-specific tool. Maybe the .gitignore should be a default file when creating an RoR project.
Are you suggesting that Github starts tracking all major frameworks, all versions of said frameworks, and the files that should maybe not be version controlled within each of those frameworks/versions?
*(which is much more sensible than proposing changes to git/github in response to a Rails default configuration problem)