Congrats, that's wonderful news.
I have had 4 beautiful babies whilst suffering from Ulcerative Colitis. I was on meds some of the time (prednisone, but tappered off fairly quickly) and my daily dose of Pentasa throughout the entire pregnancy. All were born 8.5lb or more and have no effects.
For some reason pregnancy seemed to make my colitis lie dormant so here's hoping the same will happen for you guys.
Be sure to get a great obstetrician who can communicate with your wifes GI and manage the pregnancy together.