Yes, if you look at your map you'll see that Lyon is by-passed using the A46 (on my map though the road numbers may have changed). This starts just south of Villefranche sur Saone and goes around to the east of Lyon, rejoining the A6 just north of Vienne. We found it used to take such a long time that we preferred the tunnels through Lyon itself, though!
However, depending on where you're going in the South there are lots of alternative ways using other autoroutes such as the A75 or the A20 if you're going further west than the bottom of the Rhone Valley.