I haven't heard that there is an option to just get the stones out. And if they could just remove the stones, you're still going to be very miserable trying to recover from the surgery. I don't know how everyone else handles surgery, but my body makes it clear that it does not like to be cut open!
Try the flushes!! I'm going to be doing my 3rd flush, within 3 weeks, this weekend. I started out with having a lot of pain, and finally several days after my 2nd flush, I started to feel the pain lessen. I still have some pain, and I don't expect it to go away overnight. After all, these problems didn't happen overnight. Some people see results immediately, some people it seems to take awhile.
There are lots of natural options that you have, don't let doctors tell you otherwise!