I have been
taking prilosec during my entire
pregnancy. My GYN was aware that I was on it prior to getting pregnant, and he recommended I stay on it to prevent heartburn. He said for me, the benefits outweigh the risks. I have been diagnosed with GERD. Definitely discuss it with your doctor.
You may actually find that being pregnant may help with IBS. I have read that alot of people have resolution of their symptoms during pregnancy on the Crohn's/Colitis forum.