I also tested positive for this during my second pregnancy and had the IV antibiotics during labor. I didnt flare right away, but about
8 weeks postpardum went into a terrible flare. It probably wasnt from the antibiotics though since it was so much later.
I also had antibiotics during my first labor for another reason (Dr thought my water had broken days earlier) and never had a flare after that labor and it was long so I was exposed to antibiotics for a long time that first time around.
So I think its best to go with what your Ob reccommends, but I would defintely discuss your concerns with him/her and find out if there are choices are far as which antibiotics can be used and discuss with your GI was well. And ask to have your probiotics cleared ahead of time as allowable meds in the hospital (if you sneak them in they are supposed to confiscate them).
Good luck, I wish you a speedy and healthy labor and delivery.