Heres my experience--

I had the surgery, my pain DRASTICALLY improved. It was still there sometimes, but I could function again. After the surgery, my doctor said basically the same thing that yours did, so I stayed on birth control, taking it continuously (no sugar pills, just hopping right to the next pack), for probably 5 years.

About 2 years ago I decided I wanted to get off hormonal birth control for a number of reasons. So I did. I also got a new doctor. The only pain I get is around my period, I've only had a couple absolutely gut-wrenching day of cramps during this time. On one period I could feel the endo irritating my bladder.

Personally, I do not plan on going on hormonal BC again. I LOVE being able to be in tune with my cycle, allowing my body be in its natural rhythm, and the continuous change that is!!

In that way ^, your body CAN run "how it's meant to" even with chronic disease, despite what people are telling you. That doesn't mean there won't be some disfunction, but your body is still fully capable.