Looking closely at the information you have provided it is quite clear that your daughter has growth failure and cause is growth hormone deficiency. Her height percentile is below 3% which means that out of 100 girls of her age she will be among the three shortest.
Treatment of GH deficiency is GH therapy, which is given as subcutaneous injections daily for a long time preferably till age of 14 years or her bones fuse or height gain per year is < 2 cm. With growth hormone therapy she is likely to grow 6-8 cm/year. As of today there is no substitute for GH. Medications like clonidine, high protein diet and Calcium/Vit D supplement might help.
Coming to the question of safety of GH therapy, it has been in use for more than two decades and is overall safe. Benefits are far more than the risks. Children gain weight, there is water retention, there may be slipped epiphysis of the femur bone (at hip). There are no increase in chances of Diabetes Mellitus and cancer as per the data available today.
Only inhibiting factor for this medication, especially in Indian context, is cost of therapy. If that is not the concern then your daughter is a candidate for GH therapy.