This is a lovely idea, but I agree with Lucy that it would be in very bad taste to include this info on your invitations. You will need to rely on word of mouth. Tell everyone in your family, his family, and your wedding party what your preference is and hope it gets around. If someone directly asks you what you'd like, or where you're registered, tell them about your charity.
But, please remember that you cannot dictate to people what gift they give, if they give one. Your purpose in inviting guests to your wedding is to share your day with them.