Is it just me, or does that medication seem a little strong for a baby? I'm wondering though, did the doctor test/find bacteria as the cause of your child's symptoms? The Flagyl website indicates that usual therapy is 7-10 days, Crohn's disease is not an approved indication for Flagyl, Flagyl is carcinogenic in rats and mice, and that unnecessary use should be avoided.
Did your doctor suggest perhaps your baby is allergic to what she is eating/drinking? Is she on formula or cow's milk? eating any grains? Has she ever been on antibiotics? I would have a hunch that she may have a fungal infection (antibiotics are fungal metabolites) and the milk and grains she is eating are feeding it. Flagyl would not be the first thing I would prescribe, 'IF" that was the case. Flagyl is an antibiotic, which causes yeast overgrowth. Could the rash/pain be an indication of that? But, I am not a doctor. I just know that fungus is often overlooked with GI symptoms and rashes. The Flagyl would not make the virus bug less severe, as you were wondering, if she had a virus.
As a parent, it is so difficult to see your precious baby suffering like that. It's just me, but I would be hesitant to give my baby a drug that is heavily cautioned, as the first line of defense, especially if bacteria wasn't proven to be causing the inflammation. Has your child been tested for celiac's disease, lactose intolerance? I would try an elimination diet, one without grains and cow's milk. If you notice an improvement, you may be onto something. You may not find your answer without experimenting, and your doctor may not make that suggestion to you. Mine never did, but I eventually learned on my own that diet was "the" factor in my symptoms. I'd also suggest probiotics for your little one, especially after taking a strong antibiotic.
The question that keeps coming back to me is, has your baby ever taken antibiotics before? I hope your baby feels better soon. It breaks my heart when babies are sick. They just can't tell us what is wrong, and we feel so helpless. Lots of well wishes going your way............ :)