How long was he in PT? Did his PT give you any prognosis or other information related to the expected rate of progress? Generally, insurance companies or schools want therapists to have goals for children. That way you know what is expected to happen, and by what date - then you can see if your son is getting to where he needs to be, or if the goal is something you even care about. It may be worth another shot, if you find a PT who meshes well with your family. It can take time to work, and some PTs don't work well with children. However, there are amazing PTs out there. Some kids just never do benefit from therapy, even with the best therapists. So basically, it depends, but sometimes it can be really helpful.
The orthopedist may be a good place to start. You definitely don't need to go the whole allopathic route, but having someone who is a specialist on these types of issues may give you some good input, even if you decide to address it differently than the specialist recommends.
As far as the concern with his bones, how is his diet other than the high dairy intake?