Yeah, sure, you can have multiple versions of Ruby and the Nokogiri gem on the same box. libxml2, borrowed from the GNOME project, is the C library that is doing all of the heavy lifting underneath. If the version of libxml2 on your dev machine is different than the version in prod, it doesn't much matter if you've got the same version of Ruby and the same version of Nokogiri.
Use Vagrant. You will get a complete Linux VM for each different project that will match up perfectly with whatever the prod environment looks like.