If he disagrees with the IV iron, then see her primary MD and get it done. I find it hard to believe that any GI would want their IBD patients to suffer by taking an iron pill instead of the IV infusion. Her GI should know this already that iron is hard on the gut and it causes great discomfort.
I have a hematologist as well & she suggested it. She sends my office visit reports to my GI's office so he'd be kept in the loop as well as my primary MD. They both supported her as it's the best way to get iron in my body.
If your daughter's GI doesn't listen, then get a 2nd opinion. As IBD patients, we are entitled to be made comfortable when flaring, seek out other options that will get us in remission, and if need be, a 3rd opinion may be warranted if both MDs don't listen to your concerns.
If her GI doesn't like that she's on LDN, why did he put her on it? oh, I'm on folic acid as well as it helps with the Crohn's and even clotting disorders.