Just returned from my third Franklin River rafting trip with Brett/Water by Nature. An adventure of a lifetime and great food to boot! Brett ('the chef") has rafted the river more than 200 times and probably more than any human being ever. Brett is super human in his knowledge of the river and its moods. It is a dangerous and beautiful river but with Brett I always feel I am in safe hands (I would be wary of other operators with less experience of the river).
So do the trip (either upper half or lower half - I have done both, or the full trip) and you will never regret it. It is equal to my trips around the remote Kimberley and amongst the wildlife in the Okavango Delta in Africa.