There are so many different ways to have a green wedding that you cannot say off the bat that an eco-friendly wedding will cost more or less than a conventional wedding. It really depends on the choices you make along the way (which is why I offer options marked $, $$ and $$$ in each category in The Green Bride Guide book.) To be on the safe side, I would use a traditional budget calculator, and as you make your arrangements adjust up or down.
Here is a new easy tool to help you get started.