Generally, the GI/rheumatologist makes the decision about surgery. My daughter has had two surgeries in the last two years.
Her first one was a J tube surgery, which is an open abdominal surgery - about a 2.5 inch incision through her belly button. It was an urgent surgery, since she was so malnourished and was losing weight fast. We did not have time to take her off her biologic or Imuran or even Entocort.
It took 3-4 days for her bowels to "wake up" after surgery. We were in the hospital 5 days. She did not have any issues with infections, even though she was also on a steroid.
The second surgery, an arthroscopic hip surgery, was done just 3 weeks ago. She was made to stop Cimzia two weeks before the surgery. She flared right after the surgery because she had been off it. I think it was unnecessary to stop Cimzia, but that's what her GI recommended. She healed pretty quickly and is doing well, though her IBD is still flaring (mildly).
In both cases, the surgeons deferred to her GI and rheumatologist and let them make the decisions.
On a somewhat unrelated note, she found the abdominal surgery much harder to recover from than the hip surgery. The hip surgery was a much more minor surgery (arthroscopic vs. open), but abdominal surgeries are tough because you use your abdominal muscles for basically everything.
With her abdominal surgery, she found sitting up very difficult, standing was hard and anything that used her abdominal muscles HURT - like coughing or laughing or even going to the bathroom.
For both surgeries, she was given a pain pump. With the abdominal surgery it was a regular pain pump, for the hip surgery, it was through an epidural. Pain was much better controlled with the epidural.
With the abdominal surgery, her bladder "went to sleep" from the anesthesia and she had to be cathed twice (straight cath) because it hadn't woken up and she couldn't pee. This is quite common but we didn't know about it and she was NOT happy.
For the hip surgery, we warned them that urinary retention had been an issue with M in the past, so they put a foley in while she was asleep, during the surgery. That went much more smoothly and by day 2 it was out and she was peeing.
Sorry, didn't mean to write so much. Good luck with the surgery! Let us know if you have other questions.