I've found that most organic (bio) stores have a gluten-free (sans gluten) section. Other ideas are most welcomed!
Here are a few bio addresses in Lyon:
10 rue Chavanne
69001 Lyon, France
04 78 28 52 52
Stores can be found in Villeurbanne and the 2nd, 3rd, 4th and 6th arrondissements.
la Vie Claire
Stores can be found in the 4th, 6th and 9th arrondissements.
139 Boulevard Stalingrad