Probably the reason they did not remove your's right away is because you had emergency surgery, and that area can be hard to heal if you are weak, sick or on large doses of steroids. I almost had to an emergency ileostomy and the surgeon said I would have to get my anus/rectum removed in a second operation because they thought I would have healing issues otherwise. Fortunately, I ended up not getting emergency surgery (thanks one dose of Remicade:), so a month later when I went in for my permanent ileostomy under better terms, they removed the anus and rectum during the same operation. Mine healed up wonderfully with no problems. It didn't even hurt that much... not even when the staples were still in, which surprised me because I thought it would certainly be painful to sit. My hubby even says it kinda looks the same, the opening is just shallow and doesn't lead anywhere:) I had way more problems with my abdominal incision healing.
I bet your's will heal well too since you won't be getting it done in an emergency situation 6 months from now. I don't know how involved the surgery is to have it removed separately, but it seems like it would heal more quickly and you already have the whole ileostomy part out of the way.
I am glad I had mine sewn shut because, knowing that my ileostomy was permanent, I didn't want to deal with the occasional mucus (which I have heard is pretty normal) or worry about that little bit of tissue being left to cause problems.
-Officially diagnosed with UC in 2006, though had symptoms since 1999.
-Had mild/moderate symptoms continuously until severe flare in autumn 2010 which required 2-week hospital stay
-Took Asacol, Rowasa, Canasa and Prednisone to manage flares but meds stopped working
-Tried 1 infusion of Remicade but had excruciating joint pain and discontinued
-Had permanent ileostomy surgery 11/8/2010