For anyone who has been diagnosed with endo thats too difficult to remove, I would strongly recommend going to an endo specialist for a second opinion. They treat the most complex cases, often in conjunction with a bowel surgeon, whereas less experienced surgeons will jump straight to a hyst because they don't have the skill to perform the surgery themselves.
Excision surgery to cut out the deposits by a specialists, in conjunction with a bowel surgeon to treat the endo on and around the bowel, should most definitely be tried before a hyst is even discussed. Hysterectomy is not a cure - although it helps some women, others end up in a far worse state than they were in before the surgery, especially if the surgeon has not removed every trace of endo. If they leave behind endo around the bowel for example and perform a total hyst, that endo is likely to still cause problems. If you take HRT to ease the difficult effects of an early surgical menopause, the HRT can feed the endo and cause it to grow and spread. Even women who don't take HRT can sometimes find that the endo spreads after the ovaries are removed and they don't know how. The adhesions that result from this surgery can also cause extreme pain and this is very difficult to treat.
I've been diagnosed for nearly 10 years and have spoken to lots of ladies who've had hysts - based on their stories I would never have my ovaries removed unless there were no other options and I was convinced it would help. I probably wouldn't have my uterus removed as its pointless (the endo is outside it, not in it!) unless they found I had adenomyosis, although this can be hard to diagnose.
If I was considering a total hyst, I would at the very least ask if I could take a long course of zoladex first, to see how that affects my symptoms and how I'd cope with the menopausal symptoms, especially if you're planning to go without HRT. If zoladex doesn't help, having surgery probably won't either, especially when you factor in adhesions and nerve damage from major surgery, and at least zoladex can be stopped.
If your gynae ever says that your endo is too complex to remove, they should refer you to someone who possibly can do it - if they don't, ask your gp to refer you to one of the national centres like Oxford. At the very least, let them do an MRI since severe endo is often visible on an MRI to see if they think it's likely to be treatable, before agreeing to a hyst. Personally I'd ask them to try excision before I even considered radical surgery.
As for the presence of a bowel surgeon, you may not need a resection and even if you do, that doesn't necessarily mean you'll need a bag etc. I know quite a few ladies who have had bowel resections without any major problems. In most cases, having a bowel surgeon who can treat the endo on or around the bowel avoids complications - if you have endo inside the bowel, they may have to perform a resection but it depends on your individual case.