Despite what the title suggests, this is related to the pg gem. Honestly :-)
In summary, requiring pg before Nokogiri results in the warning above. I've created a gist containing the steps required to reproduce the warning: https://gist.github.com/2236861
I've looked through the source of the pg gem and can see no explicit reference to libxml: I'm assuming that including some of the postgres headers results in libxml being loaded. Is there anything I can do to ensure that libxml 2.7.8 is being loaded, rather than 2.7.3?