How do you handle photos at the church?

My fiance and I are getting married this summer at a local church and have large guest list. We booked our photographer only for the ceremony and after-ceremony photos of ourselves and family members. Our reception is not "immediately following", but about 3 hours later at a different venue. I am stumped on what to do regarding having the guests vacate the church so we can take traditional photos at the alter with bride/groom and wedding party only.

I also have guests who have told me they will not be able to make it to our reception, and I would like to see them on the wedding day and thank them for coming, etc.

My only idea is that my groom and I walk back down the aisle and stop in the church foyer, so we can get hugs/handshakes etc from people who can't come to the reception (I know there is usually a reception line at the actual reception, but we will miss out on seeing some people!). The problem is our large guest list and waiting for everyone to exit the church so we can take pictures uninterrupted.

If anyone has any ideas/suggestion, please help! thanks!