I created a small Unity Editor Script that renames .atlas files on import to .atlas.txt. Deletes the old file if it already exists.

https://gist.github.com/talecrafter/7656531

Put that Script in an "Editor" folder in your project and it should work automatically.
I have not much experience in editor scripting, so if someone sees a flaw in this please tell us.
Tested on Windows.