If you are using a non-denominational wedding chapel, perhaps owned by a town or historical society, you may take a few liberties as long as the wedding chapel is left exactly the way it started. For instance, if there are pictures or furniture of a religious nature (i.e. a baptismal bowl or image of a religious figure), do not remove them, if at all possible. Instead, cover them tastefully with a white sheet or place flowers in or around the baptismal fixture, demonstrating your respect for the item, but indicating you are not using it for the purpose it was intended.
Decorating the wedding chapel should not be an issue that causes a great deal of stress. Floral arrangements at the chapel should be carried to the reception. Never leave items in the wedding chapel - clean up is your responsibility. If you are looking to add some classy touches for your guests, consider adding a small pin or decoration to each program, and having them on the chairs when guests sit down. Another very elegant addition would be to have a rose on each chair, or to have your ushers offer a rose to each girl, female teen, and adult woman.