Thanks to Heiko Voigt there is a bugfix for the behavior. We fixed this at the Git-Merge conference - thanks to GitHub for organizing this. The patch is pending on the mailing list at the moment. As soon as it is merged and released I am going the update this post here.
- http://www.mail-archive.com/git@vger.kernel.org/msg25556.html
- http://github.com/hvoigt/git/tree/hv/git-gui-fix-no-newline
Finally, gitgui-0.18.0 has been merged into git v1.8.4 and is part of the official release (Aug 23, 2013). Now everybody can enjoy staging linewise commits regardless of a new line at the end of the file. Thanks again to Heiko!