Hi there!
Well, without knowing the relevant clinical details or a detailed clinical evaluation it would be difficult to comment specifically on the situation; though I would tend to agree with your doctor that a surgery would be the best suitable option for bone related defects. Though physiotherapy and yoga may help in improving muscle tone and partial symptomatic improvement, these would not help treat the primary cause. I would suggest discussing the situation and the suggested management plan in detail with your treating orthopedician.
Hope this is helpful.
Take care!