There are some options in how to deal with it that this info from the Mayo Clinic may be helpful:

Ganglion cyst Definition - Diseases and Conditions - Mayo Clinic

I have had to have one removed that was so painful on my toe and one that is still not causing pain on my wrist, so am just waiting it out. My father had one surgically removed on his wrist and a friend just gets pain injections/meds for hers in her wrist. Another friend had an injection of an enzyme to dissolve it. Another friend treats it like he does his carpal tunnel with warm compresses and that seems to help beacuse it is pressing on the nerve that causes the pain.

If your doc won't help with it, find one that will as there are options to help and to be more comfortable with it or remove it. I hope you find some relief soon and don't take no for an answer; you deserve the help you need!