Be upfront about your rules and expectations:
If there are any parts of the ceremony that you are uncomfortable with, or would rather not be a part of, let it be known right away. One of the first things I tell my couples is that I don't incorporate religion into my portion of the ceremony. This usually is not an issue. If the couple is using a friend/family member for the ceremony, they probably weren't interested in a very religious ceremony anyway. However, many people still want a short prayer, a reading, or some other form of religious scripture as part of the ceremony. In this case, the best solution is to have someone else perform the religious reading. You can easily work a transition into the script where you give the floor to someone else to read a passage, a poem, sing a song, whatever. Once they finish, you continue on with your portion of the ceremony. The First-Time Officiant eBook outlines in detail the steps for a flawless transition from one speaker to another, as it can get a little tricky. Other speakers really add to the ceremony, and give you a great opportunity to take a break and catch your breath. Also, it adds some length to the ceremony which is good, because weddings officiated by amateurs tend to be a little short.