There is tremendous research going on to assess the benefits of stem cell therapy in various diseases including Hirschsprungs disease, because this disease is basically a defect of neural crest stem cells which have not migrated to the lower gut to produce ganglion cells.
The worry with embryonic stem cell therapy is the risk of forming cancer cells too. Till hard data comes, one can’t advise stem cell therapy. Alternative sources like hair follicles etc. are being investigated. But it is certainly an option for the near future.