Can't Hard Link the gitconfig File

Try Eli Barzilay's solution in his comment at http://www.xxeo.com/archives/2010/02/16/dotfiles-in-git-finally-did-it.html:

So I’ve finally found a solution that takes the best of both: put the repo in a subdirectory, and instead of symlinks, add a configuration option for “core.worktree” to be your home directory. Now when you’re in your home directory you’re not in a git repo (so the first problem is gone), and you don’t need to deal with fragile symlinks as in the second case. You still have the minor hassle of excluding paths that you don’t want versioned (eg, the “*” in “.git/info/exclude” trick), but that’s not new.

This is completely normal, and is in fact the recommended way to overwrite config files. Git creates a temporary file, writes out the config, and then moves the new file over the old one. This way, you don't get an incomplete config file (data loss) if Git gets interrupted.

You can always write a script to copy or link your config files into your central repository.

Checkout this answer, perhaps it may be of help:

https://stackoverflow.com/a/3731139/1431696

In the meantime, have you considered doing the links in reverse? Create your repository full of config files, etc, and then in the place that you actually use your files, create a hard link to the 'real' file, which sits in the repository.