I might chime in as an internal medicine resident that fecal transplantation is relatively new, and most doctors still only think of it being used for recurrent c diff (clostridium difficile) infections (which is a very bad diarrheal infection that is associated with antibiotic use and just being in the hospital).
It sounds like you are doing a good job bringing this up and questioning why your doctors are choosing certain therapies for your wife. There's more and more data coming out on using fecal transplants in Ulceratic Colitis (UC) patients and for the most part it seems well tolerated (there is one case report I just saw of someone getting a fecal transplant for c diff and then having a flare of their UC after it was in remission for 30 years).
Keep pushing and when they say no ask them why they don't think this is appropriate to try rather than the risks of surgery. It sounds like you've already done research online about this and are well informed. If her doctors aren't open to trying this (or can't because their hospital doesn't have experience doing this) I'm sure they would be able to refer you guys to someplace that would try it. Of course, there's the whole insurance issues of covering this (new and still experimental) which I won't get into but maybe there is a research study you can join.