You should absolutely discuss your concerns with the minister. A wedding is a celebration; the ceremony should bring people together and not be divisive. Be forthcoming with your minister and let him know that you want the ceremony to be as neutral and inclusive as possible. It can be done. If he insists on preaching, find a new minister and location.
My wedding was Saturday evening, and our officiant was a chaplain who agreed to do a non-religious ceremony for us. My family is Christian, my husband's family is Hindu, and we're both agnostic. We have friends who are Christian, Hindu, Muslim, Jewish, Buddhist, and atheist. It was extremely important for our wedding to make everyone feel comfortable and included. All we had to do was explain to the chaplain what we wanted. He gladly did the ceremony we asked for, and it was perfect!