You’ll need to either remove the offending URL from your history, or use the correct URL enough times to override the other one (ie, make it most-visited).
Removing the bad one is quicker and simpler, so open the History page and click the Edit items… link to the right. Now select the entry with gihub.com and click the Remove selected items… button at the top of the page. (Consider restarting Chrome to be certain that it is using the updated history.)
If you visited it too long ago and cannot find it easily, you may want to use a History-page extension such as History2, History 2, or eHistory to simplify editing the history.
[del]while targeting/hovering that entry? – ragnq Aug 26 '11 at 21:12