Most cysts including a Ganglion Cyst will go away on it's own without treatment however it can become painful if the Ganglion Cyst compresses a nerve and then you'll need surgery to remove the Ganglion Cyst.
During the surgery to remove the Ganglion Cyst your surgeon should sedate you so you don't feel anything.
That's what my surgeon did is sedate me and I didn't feel a thing during the Ganglion Cyst removal.