As a hoof care practitioner I've rehabilitated a couple of 'navicular disease'(diagnosed with nav. bone degeneration) horses, along with many more with 'navicular syndrome'(unexplained heel pain). I believe the 'natural' approach is definitely the best for these horses.
It appears from recent research that nav bone & DDFT damage is a *symptom* of the problem, rather than a cause. It also appears that it is not the cause of the pain, and while it doesn't seem likely that bone degeneration or tendon damage can be reversed/repaired, a horse can become sound & pain free despite it.
Heel pain is most commonly due to underdevelopment of the digital cushions & lateral cartilage. Management is the main consideration, as lack of exercise & good hoof function lead to lack of development. When a horse has weak digital cushions, he tends to 'tippy toe' - that is, avoid heavy impacts on his heels and land toe-first. This further lack of use can cause the heels to fall further from use, grow longer, allow the heels to become contracted & thrushy. The toe-first impacts appear to be the cause of subsequent tendon & then bone damage. It is also likely to lead to founder.
So... vets & farriers have found that padding, bar shoes, then when that no longer works growing overlong heels, then wedging heels even further out of use do indeed give the horse some comfort. However, as you can see, this treatment is palliative at best and can lead to further problems in the future.
I would advise studying hoofrehab.com & other sources of good information about hoof function & soundness, and considering keeping your horse bare(but booted/padded when necessary for comfort) and getting her *well* & frequently trimmed for starters. If you would like to post a variety of angles of hoof pics, we could give you a critique on them, for more ideas about what might be going wrong.