In your specific case, I second silentghost's suggestion. I never keep live copies of my config files in the repo, only template files. This has other benefits: You will never accidentally overwrite your production config files on update, you can keep sensitive info like database passwords out of the repository, and everyone can have their own development setup that suits their needs/preferences. When a new config line is required, just check it into the template and notify the other developers they need to merge it with their local copies. (Or, maybe look at abstracting the config file into one that changes with each environment (db connection, etc.) and one that doesn't change (constants, language vars, etc.) and that can be part of the repo.
That said, for the general need to merge a single line change into the repo, Orbman and jeffamaphone are correct. (Orbman would get my vote for most comprehensive answer, but I had already voted for SilentGhost.)