We've done antibiotics for the exact same reason twice!! She always has diarrhea, nausea and usually belly pain with antibiotics. She is generally pretty miserable till she is done with them.
My daughter has had CDiff twice and it is NOT fun. That's the big risk with antibiotics. Certain antibiotics are more likely to cause it, so do talk to your GI and make sure whatever they're giving him is not the most likely to cause CDiff.
For what it's worth, Ceftin is what caused her CDiff the first time. That whole class is more likely to cause CDiff. We avoid them now.