Before you panic, consider the likelihood that this is happening is low. There was only one study that showed this, and that was for very high doses, and mostly with quinidine. Drug addicts have tried it with pepper, and yes, Prilosec, but again, with huge doses of loperamide. It is more likely that this is a safe combination.
http://www.ncbi.nlm.nih.gov/pubmed/20604828Still, omperazole is not something you want to stay on indefinitely unless it is really needed. That is because it can interfere with B-12 absorbtion by lowering the stomach acid too much. I'd talk this over with his GI to see what the best option would be.
Kids are notorious for not being cooperative with eating, regardless of what is going on healthwise. She may just be doing the normal kid stuff that is frustrating.
Jan