I believe it would be useful for you to delete the highest-level "geshi" directory within your plugin and move the contents up to the plugin root directory. This would allow people who have host-wide GeSHi installations in their PHP include path (i.e. /usr/share/php/geshi.php) to simply "rm -Rf geshi.php geshi" and use their server-wide GeSHi. People who don't wouldn't see any changes.
I've detailed the exact suggested changes on my blog: