Your attendants do not have to enter the church in pairs. I have had attendants walk in trios and some processions have the attendants enter individually. It is your day, so whatever you prefer is fine.
Yes, tradition has it that all of the bridesmaids stand to the left of the bride while the groomsman stand to the right of the groom but there is no penalty for veering from the norm. The above picture shows how you can eliminate such a quandary of having uneven attendants.
I would suggest giving your photographer a heads up so that he may think of some creative ways to photograph the wedding party. The wedding party may be placed behind the bride and groom in a semi-circle or staged photography (acting out a scene). A good photographer will know how to work with this situation.
Make It Memorable!