One thing we found out early on in our photography career was that some churches, some pastors, and even some parents are very opposed to photography (especially flash photography) during the ceremony.  While we are sensitive to these requests, it can make it difficult for us to do what we feel that we have been paid to do, which is capture the wedding day and ceremony as it happens.  We don't mind taking a break during the ceremony as long as the couple and family knows this up front and expects minimal ceremony pictures.

This is just something that you will want to keep in mind when you talk to your minister.  If you would prefer photos of your ceremony, just make sure that you communicate that to the minister.  Even if they don't want us to use flash, sometimes they will let us shoot without flash, but unless your church has a lot of natural light, the pictures won't be quite as good as they would with flash.  The other important thing would be to relay the conversation you have with the minister to your photographer so that they are in the loop.  We can't honor these requests unless we are made aware of them. 

This is usually a concern in Catholic churches and among more traditional denominations, but just make sure you ask as it may or may not be an issue in your particular church.