we have spent in provence and traveled up/down from the franche-comté region and stayed in some really nice small inns, didn't do any river traveling though. if you can pick up a copy of a "relais du silence" guidebook you won't be sorry ... we never had a problem with any of the places we stayed, and the food was always great.
if you can go a little east to toulouse, make sure you go to a pastry shop and ask for "un cochon" you won't be sorry