Because what you need to theme is the display of the field itself, I think your best option is to create a custom module that implements a new formatter for nodereference. Then for your field, you can just select that formatter under display options (or whatever it is called).
I've never created a formatter before, but a bit of Googling revealed this article: http://manueg.okkernoot.net/blog/200907/how-create-cck-formatter
You could also very easily look at the nodereference module itself and see how it implements its current formatters (full node, teaser, etc.).
Hope that helps!